QPix 420 Colony Picking System User Guide

Transcription

QPix 420 Colony Picking System
User Guide
5026152 A
March 2013
This document is provided to customers who have purchased Molecular Devices®, LLC
(“Molecular Devices”) equipment, software, reagents, and consumables to use in the
operation of such Molecular Devices equipment, software, reagents, and consumables. This
document is copyright protected and any reproduction of this document, in whole or any part,
is strictly prohibited, except as Molecular Devices may authorize in writing.
Software that may be described in this document is furnished under a license agreement. It
is against the law to copy, modify, or distribute the software on any medium, except as
specifically allowed in the license agreement. Furthermore, the license agreement may
prohibit the software from being disassembled, reverse engineered, or decompiled for any
purpose.
Portions of this document may make reference to other manufacturers and/or their products,
which may contain parts whose names are registered as trademarks and/or function as
trademarks of their respective owners. Any such usage is intended only to designate those
manufacturers’ products as supplied by Molecular Devices for incorporation into its
equipment and does not imply any right and/or license to use or permit others to use such
manufacturers’ and/or their product names as trademarks.
Molecular Devices makes no warranties or representations as to the fitness of this equipment
for any particular purpose and assumes no responsibility or contingent liability, including
indirect or consequential damages, for any use to which the purchaser may put the
equipment described herein, or for any adverse circumstances arising therefrom.
For research use only. Not for use in diagnostic procedures.
The trademarks mentioned herein are the property of Molecular Devices, LLC or their respective
owners. These trademarks cannot be used in any type of promotion or advertising without the
prior written permission of Molecular Devices, LLC.
Patents: http://www.moleculardevices.com/productpatents
Product manufactured by Molecular Devices, LLC.
1311 Orleans Drive, Sunnyvale, California, United States of America 94089.
Molecular Devices, LLC is ISO 9001 registered.
© 2013 Molecular Devices, LLC.
All rights reserved.
Contents
Safety Information . . . . . . . . . . . . . . . . . .
Warning and Caution Definitions . . . . . . . .
Maintenance . . . . . . . . . . . . . . . . . . . . . .
General Precautions. . . . . . . . . . . . . . . . .
Health and Safety . . . . . . . . . . . . . . . . . .
External or implanted medical device risk .
Transport and Storage . . . . . . . . . . . . . .
Lifting Points . . . . . . . . . . . . . . . . . . . . .
External Covers . . . . . . . . . . . . . . . . . . .
Electrical Safety . . . . . . . . . . . . . . . . . . .
Electrical Safety . . . . . . . . . . . . . . . . . .
High Voltage . . . . . . . . . . . . . . . . . . . . .
Disposal of Electronic Equipment . . . . . . .
Chemical and Biological Safety . . . . . . . . .
Moving Parts. . . . . . . . . . . . . . . . . . . . . .
Cleaning. . . . . . . . . . . . . . . . . . . . . . . . .
Safety Features. . . . . . . . . . . . . . . . . . . .
Door . . . . . . . . . . . . . . . . . . . . . . . . . .
UV Light . . . . . . . . . . . . . . . . . . . . . . . .
Emergency Stop Button . . . . . . . . . . . . .
Drive Safety . . . . . . . . . . . . . . . . . . . . .
Hot Air/Halogen Dryer . . . . . . . . . . . . . .
Noise Levels . . . . . . . . . . . . . . . . . . . . .
Biohazard . . . . . . . . . . . . . . . . . . . . . . .
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Chapter 1: Introduction . . . . . . . . . . . . . . .
Overview . . . . . . . . . . . . . . . . . . . . . . . . .
Using the QPix 420 Colony Picking System .
Functionality of the QPix 420 System. . . . . .
Picking . . . . . . . . . . . . . . . . . . . . . . . . . .
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Chapter 2: Software Overview . . . . . . . . . . . . . . . . . . . . . . . . 17
The QPix 420 Colony Picking Software . . . . . . . . . . . . . . . . . . . 17
Navigation Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Menu Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
View Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Tools Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Right Menu Column - Current and New Processes . . . . . . . . . . 18
Gridding Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Barcodes Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Head Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Microplates and Filters Window . . . . . . . . . . . . . . . . . . . . . . . 20
5026152 A
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Contents
Filter Design Window . . . . . . . . . . . . . . . . . . . . . . . .
Filter Layout Window . . . . . . . . . . . . . . . . . . . . . . . .
Substrate Window . . . . . . . . . . . . . . . . . . . . . . . . . .
Holder Layout Window . . . . . . . . . . . . . . . . . . . . . . .
Load Plates Window . . . . . . . . . . . . . . . . . . . . . . . . .
Settings Summary Window . . . . . . . . . . . . . . . . . . . .
Standard and Regional Picking Processes . . . . . . . . . . .
Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . .
Filter Pairs List . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Barcodes Window. . . . . . . . . . . . . . . . . . . . . . . . . . .
Destination Options Window . . . . . . . . . . . . . . . . . . .
Destination/Source Options Window (Regional Picking).
Head/Sanitise Window . . . . . . . . . . . . . . . . . . . . . . .
Source Window . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Holder Layout Summary Window . . . . . . . . . . . . . . . .
Test Image Window . . . . . . . . . . . . . . . . . . . . . . . . .
FL Test Image Window . . . . . . . . . . . . . . . . . . . . . . .
Feature Selection Window . . . . . . . . . . . . . . . . . . . . .
Feature Counts Tab . . . . . . . . . . . . . . . . . . . . . . . .
Display Options Tab . . . . . . . . . . . . . . . . . . . . . . . .
Control Plate Creation Processes . . . . . . . . . . . . . . . . .
Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . .
Barcodes Window. . . . . . . . . . . . . . . . . . . . . . . . . . .
Destination Options Window . . . . . . . . . . . . . . . . . . .
Head/Sanitise Window . . . . . . . . . . . . . . . . . . . . . . .
Source Window . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Control Plate Window . . . . . . . . . . . . . . . . . . . . . . . .
Holder Layout Summary Window . . . . . . . . . . . . . . . .
Test Image Window . . . . . . . . . . . . . . . . . . . . . . . . .
Feature Selection Window . . . . . . . . . . . . . . . . . . . . .
Replication Processes . . . . . . . . . . . . . . . . . . . . . . . . .
Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . .
Barcodes Window. . . . . . . . . . . . . . . . . . . . . . . . . . .
Microplates/Sanitise Window . . . . . . . . . . . . . . . . . . .
Head Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Rearraying Processes . . . . . . . . . . . . . . . . . . . . . . . . .
Routines Window . . . . . . . . . . . . . . . . . . . . . . . . . . .
Barcodes Window. . . . . . . . . . . . . . . . . . . . . . . . . . .
Source Window . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Destination Window . . . . . . . . . . . . . . . . . . . . . . . . .
Head and Sanitise Window . . . . . . . . . . . . . . . . . . . .
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5026152 A
Settings Summary Window .
Data Viewer Processes . . . . .
Data Viewer . . . . . . . . . . .
Database Management. . . .
Manage Sanitise Profiles. . . .
Camera Alignment Process . .
Instrument Utilities . . . . . . .
Change Head . . . . . . . . . .
Pin Fire Test . . . . . . . . . . .
UV Sanitise Window . . . . . .
Sanitise . . . . . . . . . . . . . .
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41
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Chapter 3: Instrument Maintenance . .
Aligning the Camera . . . . . . . . . . . . .
Changing the Head . . . . . . . . . . . . . .
Performing a Pin Fire Test . . . . . . . . .
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Chapter 4: Instrument Overview . . . .
Introduction . . . . . . . . . . . . . . . . . . .
Pre-Power-Up Checklist . . . . . . . . . .
Power-Up Procedures . . . . . . . . . . . .
Shutdown procedure . . . . . . . . . . . .
Installation . . . . . . . . . . . . . . . . . . . .
Mounting the Instrument . . . . . . . . .
Instrument Layout. . . . . . . . . . . . . . .
Front Panel Display . . . . . . . . . . . . . .
Display Icons . . . . . . . . . . . . . . . . . .
Service and Maintenance . . . . . . . . . .
General Maintenance . . . . . . . . . . . .
Weekly Maintenance . . . . . . . . . . . .
Bi-annual Maintenance . . . . . . . . . . .
Cleaning Procedures . . . . . . . . . . . . .
Cleaning the Instrument Interior . . .
Incoming Compressed Air Supply . .
Automated Pin Cleaning . . . . . . . . .
Removable Parts . . . . . . . . . . . . . . . .
The Head . . . . . . . . . . . . . . . . . . .
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Chapter 5: Preparations for Running a Routine . . . . . . . . . . . 59
Preparing your Wash Baths. . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Conducting a Sanitise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Conducting a UV Sanitise . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Creating and Editing Sanitise Profiles . . . . . . . . . . . . . . . . . . . . 61
Editing a Sanitise Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Deleting a Sanitise Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Chapter 6: Conducting a Picking Routine . .
Preparing for a Picking Routine . . . . . . . . . .
Creating and Editing a Picking Routine . . . . .
Selecting Barcode Reading Options . . . . . .
Setting Filter Pairs (Fluorescent Light only).
5026152 A
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5
Contents
Setting Destination Options . . . . . . . . . . . . . . . . . .
Selecting Head and Sanitise Options. . . . . . . . . . . .
Setting your Picking Source. . . . . . . . . . . . . . . . . .
Viewing the Settings Summary . . . . . . . . . . . . . . .
Running a Picking Routine. . . . . . . . . . . . . . . . . . . .
Arranging the Layout of the Holders . . . . . . . . . . . .
Creating a White Light Test Image . . . . . . . . . . . . .
Creating a Fluorescent Test Image (Fluorescent light
Selecting Colonies . . . . . . . . . . . . . . . . . . . . . . . .
Viewing a Summary of Selected Colonies . . . . . . . .
Viewing Additional Display Options . . . . . . . . . . . . .
Continuing or Saving Your Routine . . . . . . . . . . . . .
Loading the Plate Holders . . . . . . . . . . . . . . . . . . .
Viewing the Picking Progress . . . . . . . . . . . . . . . . .
Completing or Running Another Routine . . . . . . . . .
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Chapter 7: Conducting a Regional Picking Routine . . . . . . . . . 85
Preparing for a Regional Picking Routine . . . . . . . . . . . . . . . . . . 85
Creating and Editing a Regional Picking Routine. . . . . . . . . . . . . 86
Selecting Barcode Reading Options . . . . . . . . . . . . . . . . . . . . 87
Setting Filter Pairs (Fluorescent Light only) . . . . . . . . . . . . . . . 89
Configuring Destination Microplates . . . . . . . . . . . . . . . . . . . . 89
Setting your Regional Picking Source . . . . . . . . . . . . . . . . . . . 90
Defining Destination/Source Options . . . . . . . . . . . . . . . . . . . 91
Selecting Head and Sanitise Options. . . . . . . . . . . . . . . . . . . . 92
Viewing the Settings Summary . . . . . . . . . . . . . . . . . . . . . . . 94
Running a Regional Picking Routine . . . . . . . . . . . . . . . . . . . . . 95
Arranging the Layout of the Holders . . . . . . . . . . . . . . . . . . . . 95
Creating a White Light Test Image . . . . . . . . . . . . . . . . . . . . . 96
Creating a Fluorescent Test Image (Fluorescent light only) . . . . 98
Selecting Colonies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Viewing a Summary of Selected Regional Colonies . . . . . . . . . 101
Viewing Additional Display Options . . . . . . . . . . . . . . . . . . . . 102
Continuing or Saving Your Routine . . . . . . . . . . . . . . . . . . . . 103
Loading the Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Viewing Regional Picking Progress . . . . . . . . . . . . . . . . . . . . 104
Completing or Running Another Routine . . . . . . . . . . . . . . . . 105
Chapter 8: Control Plate Creation Processes . . . . . . . . . . . . . 107
Preparing for a Control Plate Creation Routine . . . . . . . . . . . . . 107
Creating and Editing a Control Plate Creation Routine. . . . . . . . 108
Selecting Barcode Reading Options . . . . . . . . . . . . . . . . . . . 109
Setting Destination Options . . . . . . . . . . . . . . . . . . . . . . . . . 109
Selecting Head and Sanitise Options. . . . . . . . . . . . . . . . . . . 110
Setting your Source Receptacle . . . . . . . . . . . . . . . . . . . . . . 111
Designating the Control Plate Layout . . . . . . . . . . . . . . . . . . 111
Viewing the Settings Summary . . . . . . . . . . . . . . . . . . . . . . 112
Running a Control Plate Creation Routine . . . . . . . . . . . . . . . . 113
Arranging the Layout of the Holders . . . . . . . . . . . . . . . . . . . 113
Loading Source Receptacles . . . . . . . . . . . . . . . . . . . . . . . . 114
Creating a Test Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
6
5026152 A
Selecting Colonies . . . . . . . . . . . . . . . .
Viewing a Summary of Selected Colonies
Viewing Additional Display Options . . . .
Continuing or Saving Your Routine . . . .
Loading the Plate Holders . . . . . . . . . . .
Viewing the Picking Progress. . . . . . . . .
Viewing the Summary of Your Routine . .
5026152 A
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Chapter 9: Replication Processes . . . . . . .
Preparing for a Replicating Routine . . . . . .
Creating and Editing a Replicating Routine .
Selecting Barcode Reading Options . . . . .
Setting Microplate and Sanitise Options . .
Setting Head Options . . . . . . . . . . . . . . .
Running a Replicating Routine. . . . . . . . . .
Arranging the Layout for the Routine . . . .
Viewing the Settings Summary . . . . . . . .
Continuing or Saving Your Routine . . . . .
Viewing the Replication Progress . . . . . . .
Viewing the Replicating Process Summary
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Chapter 10: Conducting a Rearraying Routine
Performing Rearraying Procedures. . . . . . . . . .
Preparing for a Rearraying Routine . . . . . . . . .
Creating and Editing a Rearraying Routine . . . .
Selecting Barcode Reading Options . . . . . . . .
Identifying your Source Receptacle . . . . . . . .
Defining your Destination Receptacle . . . . . . .
Selecting Head and Sanitise Options . . . . . . .
Running a Rearraying Routine. . . . . . . . . . . . .
Confirming the Layout for the Routine . . . . . .
Viewing the Settings Summary . . . . . . . . . . .
Viewing the Rearraying Progress . . . . . . . . . .
Viewing the Rearraying Process Summary . . .
. . . . . . . . . . . 133
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Chapter 11: Gridding Processes . . . . . . . . .
Preparing for a Gridding Routine . . . . . . . . .
Creating and Editing a Gridding Routine . . . .
Selecting Barcode Reading Options . . . . . .
Selecting Head and Sanitise Options . . . . .
Setting Source and Destination Receptacles
Creating a Filter Design Layout . . . . . . . . .
Selecting the Destination Tray . . . . . . . . .
Selecting Stamping and Inking Options . . .
Running a Gridding Routine . . . . . . . . . . . .
Arranging the Layout for the Routine . . . . .
Viewing the Settings Summary . . . . . . . . .
Continuing or Saving Your Routine . . . . . .
Viewing the Gridding Progress. . . . . . . . . .
Viewing the Summary of Your Routine . . . .
. . . . . . . . . . . 143
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116
118
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7
Contents
Chapter 12: Data Viewer Processes. . . . . . . . . . .
Conducting a Data Search. . . . . . . . . . . . . . . . . .
Searching by Tag . . . . . . . . . . . . . . . . . . . . . . .
Searching by Barcode . . . . . . . . . . . . . . . . . . . .
Searching by Date . . . . . . . . . . . . . . . . . . . . . .
Searching by User . . . . . . . . . . . . . . . . . . . . . .
Searching by Location. . . . . . . . . . . . . . . . . . . .
Viewing and Printing Settings Details . . . . . . . . .
Working with Tags . . . . . . . . . . . . . . . . . . . . . . .
Creating a Tag . . . . . . . . . . . . . . . . . . . . . . . . .
Adding Tags to a Receptacle, Location, or Routine
Removing a Tag . . . . . . . . . . . . . . . . . . . . . . . .
Adding Annotations . . . . . . . . . . . . . . . . . . . . . .
Exporting Processes or Routines . . . . . . . . . . . . .
Adding or Deleting Properties for Microplates . . . .
Adding Properties. . . . . . . . . . . . . . . . . . . . . . .
Deleting a Property . . . . . . . . . . . . . . . . . . . . .
Viewing a Map of the Locations . . . . . . . . . . . . . .
Working with Sample Trails . . . . . . . . . . . . . . . . .
Adding and Removing Sample Trails. . . . . . . . . .
Viewing and Clearing Sample Trails . . . . . . . . . .
. . . . . . . . . 159
. . . . . . . . . 159
. . . . . . . . . 160
. . . . . . . . . 160
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. . . . . . . . . 161
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. . . . . . . . . 168
. . . . . . . . . 168
. . . . . . . . . 169
Appendix A: Replacement Parts and Optional Extras . . . . . . 171
Replacement Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Appendix B: Technical Specifications
Technical Specifications . . . . . . . . . .
Electrical Connections. . . . . . . . . . . .
Dimensions of the QPix 420 System . .
...
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. . . . . . . . . 174
. . . . . . . . . 175
Appendix C: Electromagnetic Compatibility (EMC) . . . . . . . . 177
REGULATORY INFORMATION FOR CANADA
(ICES/NMB-001:2006) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
ISM EQUIPMENT CLASSIFICATION (Group 1, Class A) . . . . . . . 177
INFORMATION FOR THE USER (FCC NOTICE) . . . . . . . . . . . . . 177
Appendix D: Technical Assistance and Troubleshooting . . . . 179
Technical Assistance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Global Customer Support Center . . . . . . . . . . . . . . . . . . 179
To Inquire About a Service Plan . . . . . . . . . . . . . . . . . . . . . . 179
North America . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Europe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Key Service and Support Offices . . . . . . . . . . . . . . . . . . . . . 179
North America . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Europe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Glossary of Terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
8
5026152 A
Safety Information
WARNING! If the equipment is used in a manner not specified by
Molecular Devices®, the protection provided by the equipment can be
impaired.
Warning and Caution Definitions
All Warning and Cautions in this document include an exclamation point, a
lightning bolt, or a light burst symbol framed within a triangle.
The exclamation point symbol is an international symbol which serves as a
reminder that all safety instructions should be read and understood before
installation, use, maintenance, and servicing is attempted.
WARNING! A WARNING calls attention to a condition or possible
situation that could cause injury to the operator.
CAUTION! A CAUTION calls attention to a condition or possible situation that
could damage or destroy the product or the operator’s work.
When warnings and cautions appear in this guide, pay special attention to the
specific safety information associated with them.
Please read and observe all warnings, cautions, and instructions. remember,
the most important key to safety is to operate the QPix 420 System with care.
Maintenance
Perform only the maintenance described in this guide. Maintenance other than
that specified in this guide should be performed only by Molecular Devices
service engineers.
Note: It is your responsibility to decontaminate components of the QPix 420
System before requesting service by a service engineer or returning parts to
Molecular Devices for repair. Please contact Molecular Devices for the relevant
decontamination certificate. Molecular Devices will NOT accept any items
which have not been decontaminated where it is appropriate to do so. If any
parts are returned, they must be enclosed in a sealed plastic bag stating that
the contents are safe to handle and are not contaminated.
General Precautions
All wastes, for example ethanol, must be disposed of according to local
regulation. Ethanol is flammable and should be handled accordingly.
Do not use in explosive environments.
For safety reasons, never interfere with or override the front door switch.
5026152 A
9
Safety Information
Health and Safety
Note: Before using the QPix 420 System, Molecular Devices
recommends you read this guide to understand all safety instructions.
Prior to using the instrument, confirm all tasks listed in the PrePower-Up Checklist on page 51, to ensure all moving parts are
correctly positioned.
Molecular Devices also recommends you follow all steps in Power-Up
Procedures on page 51.
External or implanted medical device risk
WARNING! Motors and their associated drives and cabling are
sources of electromagnetic fields. Persons with external or implanted
medical devices need to evaluate the risks associated with these
devices before entering an area where they are in use.
WARNING! High magnetic field. If you have an external or implanted
medical device fitted, keep 300 mm away from drive magnets.
Transport and Storage
The QPix 420 System must be stored and transported in temperatures within
the range of -25°C to +55°C.
Lifting Points
The QPix 420 System should not be moved after installation. If relocation is
necessary, standard lifting gear is adequate but should be undertaken only in
the presence of a Molecular Devices approved engineer.
The instrument should be moved into position using appropriate handling
equipment such as forklift trucks or dolly trucks, and it should be properly
balanced on the forks prior to lifting.
CAUTION! Do not use any part of the QPix 420 System exterior body to lift
it, as this can cause irreparable damage.
External Covers
WARNING! If any of the external covers on the QPix 420 System are
removed, the power supply does not automatically stop. If you must
remove any of the external covers, you must ensure that the power is
switched off first. Do not attempt to use the instrument again until all
covers are replaced.
10
5026152 A
Electrical Safety
To prevent electrically related injuries and property damage, properly inspect
all electrical equipment prior to use and immediately report any electrical
deficiencies. For any servicing of equipment requiring the removal of covers or
panels, contact a service engineer.
Electrical Safety
WARNING! The QPix 420 System must be connected to a properly
earthed power outlet to protect users from the risk of electric shock.
The main chassis of the instrument is earthed together with all
associated electrical components.
Do not remove any of the fixed covers, as there are no user
serviceable parts inside. All electrical work should be referred to
Molecular Devices approved service personnel.
In the event of a liquid spillage into the base cavity of the instrument,
disconnect the mains power supply before attempting to clean up.
High Voltage
WARNING! This symbol indicates the potential of an electrical shock
hazard existing from a high voltage source and that all safety
instructions should be read and understood before proceeding with
the installation, maintenance, and servicing of all modules.
Do not remove instrument covers. To avoid electrical shock, use only supplied
power cords and connect to properly grounded (three-holed) wall outlets.
Disposal of Electronic Equipment
It is important to understand and follow all laws regarding the safe and proper
disposal of electrical instrumentation.
The symbol of a crossed-out wheeled bin on the product is required in
accordance with the Waste Electrical and Electronic Equipment (WEEE)
Directive of the European Union. The presence of this marking on the product
indicates that:
• the device was put on the European Market after August 13, 2005.
• the device is not to be disposed via the municipal waste collection
System of any member state of the European Union.
For products under the requirement of WEEE directive, please contact your
dealer or local Molecular Devices office for the proper decontamination
information and take back program, which will facilitate the proper collection,
treatment, recovery, recycling, and safe disposal of the device.
5026152 A
11
Safety Information
Chemical and Biological Safety
Normal operation of the instrument can involve the use of materials that are
toxic, flammable, or otherwise biologically harmful. When using such
materials, observe the following precautions:
• Handle infectious samples according to good laboratory procedures and
methods to prevent the spread of disease.
• Observe all cautionary information printed on the original solutions
containers prior to their use.
• Dispose of all waste solutions according to your facility’s waste disposal
procedures.
• Operate the instrument in accordance with the instructions outlined in
this guide, and take all the necessary precautions when using
pathological, toxic, or radioactive materials.
• Splashing of liquids can occur; therefore, take appropriate safety
precautions, such as using safety glasses and wearing protective
clothing, when working with potentially hazardous liquids.
• Use an appropriately contained environment when using hazardous
materials.
• Observe the appropriate cautionary procedures as defined by your
safety officer when using flammable solvents in or near a powered-up
instrument.
• Observe the appropriate cautionary procedures as defined by your
safety officer when using toxic, pathological, or radioactive materials.
Note: Observe all warnings and cautions listed for any external devices
attached to or in use during the operation of the instrument. See the
applicable user guides for operating and safety procedures of that device.
Moving Parts
To avoid injury due to moving parts, observe the following:
• Never attempt to exchange labware, reagents, or tools while the
instrument is operating.
• Never attempt to physically restrict any of the moving components of
the QPix 420 System.
• Keep the QPix 420 System interior clear to prevent obstruction of the
movement.
Cleaning
Note: Molecular Devices recommends you always use ethanol for cleaning,
because autoclaving is not compatible with anodized parts.
Observe the cleaning procedures outlined in this user guide for the instrument.
Prior to cleaning equipment that has been exposed to hazardous material:
• Appropriate Chemical and Biological Safety personnel should be
contacted.
• The Chemical and Biological Safety information contained in this user
guide should be reviewed.
12
5026152 A
Safety Features
Door
The QPix 420 System is equipped with an automatically locking door which
locks whenever you run any routine. The door is made from acrylic, and so
prevents UV light from passing through during operation.
As a safety measure, if the door is open, an electromagnetic switch prevents
the instrument from running. This switch should never be tampered with, as it
serves two purposes:
• It prevents the motors from running and therefore the potential of any
physical damage.
• It disables the UV light therefore preventing the risk of damage from
UV radiation.
UV Light
The QPix 420 System is fitted with a UV germicidal lamp and timer. It is a 30W
linear discharge lamp with a sharply defined output at 253.7 nm, making it an
efficient source of germicidal radiation.
Emergency Stop Button
The location of the Emergency Stop button is shown in Front Panel Display on
page 54. Pressing the Emergency Stop button immediately stops all motion
and turns off the instrument. Before you can restart the instrument, you must
pull the button out and also press the Start button.
Be sure to not block or obstruct this button.
Drive Safety
CAUTION! Be aware that the motors use high-powered magnets.
The linear drive units and encoders are delicate, so take great care with them.
Follow the Pre-Power-Up Checklist on page 51 before every routine, to prevent
serious damage to the QPix 420 System or any of its constituent parts.
All power ceases to the drives when the doors are open.
Hot Air/Halogen Dryer
The QPix 420 System is fitted with high temperature halogen dryer. The casing
can become hot during the drying cycle.
WARNING! The casing can become hot during the drying cycle.
Noise Levels
During normal operation the level of airborne noise emitted by the QPix 420
System will not exceed 70db(A) measured at a distance of 1 metre.
Biohazard
WARNING! If any biohazard is introduced to the instrument during
operation the area needs to be clearly marked with an appropriate
biohazard sign.
5026152 A
13
Safety Information
14
5026152 A
Introduction
1
Overview
The QPix 420 Colony Picking System allows you to control selective microbial
colony picking. It allows multiple users to select and collect microbial colonies
from various receptacles.
Using the QPix 420 Colony Picking System
This user guide contains all the information you will need to fully understand
and use the QPix 420 System. Please refer to the related chapters for
important setup, maintenance and safety information.
• Safety Information on page 9
• Software Overview on page 17
• Instrument Maintenance on page 47
• Instrument Overview on page 51
• Preparations for Running a Routine on page 59
• Data Viewer Processes on page 159
Functionality of the QPix 420 System
The QPix 420 instrument is part of the QPix 400 series, which also includes the
QPix 450 and QPix 460. The QPix 420 System offers available features to suit a
whole range of needs, including fluorescent imaging, regional picking,
rearraying, and compression and expansion replicating.
The QPix 420 System is available both with transmitted White Light only and
Fluorescent And White Light functionality.
Multiple fluorescent filters ensure compatibility with a wide range of
fluorescent cloning dyes and proteins, and enables both systems to reveal
unique information about individual colonies. Fluorescent imaging is available
as an option on all systems.
After colonies are located using a CCD camera, they are picked at high speed
from source plates and then inoculated into pre-filled 96 or 384 well
microplates. Selected colonies of interest can then be rearrayed from a library
into new microplates.
In order to optimize these systems, Molecular Devices® has developed a
range of plastic consumables for use with the instrument. The destination
microplate bed allows for versatile use of shallow, standard, and deep well
microplates in various combinations.
You can log all your processes such as picking, replicating, and re-arraying
with the software, which allows you to tag important samples to enhance the
history, location, and extra details of sample-specific data.
5026152 A
15
Introduction
Picking
The QPix 420 System is capable of automatically picking in excess of 3000
colonies per hour. This is achieved with an integrated vision, detection, and
analysis hardware and software System and a 96-pin head assembly, both
custom designed by Molecular Devices.
After you have identified potential colonies, the source plate is then imaged in
multiple frames using a CCD camera. These images are processed to produce
a single, large image of the colonies on the source plate. Specific colonies are
then selected for picking using feature selection parameters, such as size,
shape, and proximity.
The instrument picks from a range of source plates including large QTrays,
Omni Trays, and standard Petri dishes using the optional source plate holders.
A fluorescent imaging head is also available. This comprises an LED-based
light source that enables different excitation wavelengths to be selected using
preset filter pairs, a filter for selecting appropriate fluorescence emission
wavelengths, and a sensitive monochrome CCD camera for image acquisition.
When fitted, this fluorescence head can also be used for white light imaging
using the transmitted light source fitted below the source plate holder.
The fluorescent imaging system allows for the addition of fluorescent intensity
parameters in the selection criteria.
Note: The QPix 420 System is strictly for research use only and is not
intended or recommended for the diagnosis of disease in humans or animals.
If the System is used in a manner not specified in this manual, the protection
provided by the equipment could become impaired.
16
5026152 A
Software Overview
2
The QPix 420 Colony Picking Software
The QPix 420 software controls the QPix 420 Colony Picking System. You
access all processes and other functionality from the Navigation window, which
opens after you launch the software. The following tabs are found at the top of
the window:
• New Process allows you to create a new routine. It contains existing
QPix 420 software processes, as well as Maintenance and Utility
processes.
• Recent Processes allows you to use a previously saved routine.
The following processes can be performed using the QPix 420 software.
• Gridding Processes on page 19
• Standard and Regional Picking Processes on page 24
• Control Plate Creation Processes on page 31
• Replication Processes on page 35
• Rearraying Processes on page 38
• Data Viewer Processes on page 42
• Manage Sanitise Profiles on page 43
• Camera Alignment Process on page 44
• Instrument Utilities on page 45
This chapter describes the functionality of these various processes.
Subsequent chapters describe how to perform the various routines that are
possible within each process.
Once all systems have been correctly powered up and initialized, start the
software and connect to the QPix 420 System by double-clicking the QPix 420
icon.
Navigation Window
The Navigation window displays all processes for the QPix 420 System.
5026152 A
17
Software Overview
Menu Options
The same menu is displayed in all windows, but available items will vary.
File Menu
The only menu option that is usable under the File menu is the following:
• Exit closes the QPix 420 software.
View Menu
•
•
•
Properties displays the routine properties being set prior to starting
the routine.
Progress displays the progress of a running routine.
Administrative Properties allows you to change the Properties view
and default values.
Tools Menu
•
Configuration opens the QPix 420 software configuration settings.
Note: Molecular Devices® recommends only trained personnel
configure these settings.
•
Prepare Error Report launches a wizard that creates a data file
containing the configuration and recent log files to help Molecular
Devices troubleshoot your problem.
Help Menu
•
•
About displays the version numbers of the QPix 420 software modules.
If asked to provide the software version number, give this number
unless otherwise directed.
Online Support opens the online support web page if the QPix 420
System has an active internet connection.
Right Menu Column - Current and New Processes
These menus are applicable to other Molecular Devices products using the
same software platform. They are not applicable to the QPix 420 System.
18
5026152 A
Gridding Processes
The gridding process allows you to deposit liquid samples from one or more
source microplates to one or more destination surfaces (either agar filled
QTrays or filters).
For information on conducting a gridding routine, see Gridding Processes on
page 143.
As with other processes, you must start with creating your routine.
Routines Window
The QPix 420 software allows you to run a new or existing routine using
various pre-configured routines from the Routines window.
Barcodes Window
The QPix 420 software lets you read barcodes in various ways.
Source barcodes can be listed in any order. The QPix 420 System searches the
list to validate that the source barcode is present. If it is not, a message
appears describing the erroneous receptacle.
Note: Validation barcodes are an option for source receptacles only. Barcodes
compatible with the barcode reader are code 39, code 93, and code 128.
5026152 A
19
Software Overview
Head Window
Use the Head window for setting the gridding head and wash cycle you want
for the routine.
Microplates and Filters Window
Use the Microplates and Filters window to set up the source receptacles and
destination surface, as well as control the number of times the head dips into
the source receptacle or stirs the source solution.
Note: If the stacker icons are greyed out and unselectable in the next
window, it is because you chose an unsuitable microplate in the current
window. The software knows the specifics of the stacker lane configuration for
your instrument, and allows you to choose only suitable microplates. Return
to this current window to select a suitable microplate.
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Filter Design Window
Use the Filter Design window to create and arrange the gridding spot
patterns and the fields they will be stamped onto.
Filter Layout Window
The Filter Layout window selection options are greyed out, because you have
only the option of using one QTray.
Substrate Window
Use the Substrate window to select stamping and inking options for your
routine.
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Software Overview
Holder Layout Window
The Holder Layout window shows you how to correctly arrange the
microplate holders in the instrument for your routine dictated by the selections
made at the Source/Destination step earlier. You must click the Checked? box
to continue from this window.
Load Plates Window
The Load Plates window displays how many and what type of microplates you
need to load for your routine. You must click the Checked? box to continue
from this window.
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Settings Summary Window
Use the Settings Summary window to view the settings for your gridding
routine.
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23
Software Overview
Standard and Regional Picking Processes
The QPix 420 software allows you to pick colonies from receptacles using
either the standard or regional process. These can be performed with both
white light and fluorescent imaging capabilities if your System has been
suitably configured. Both processes are described in this section.
If you want to perform a regional colony pick, it must be done using a 48region divided Bioassay tray (for example the Molecular Devices QTray
(X6029)). For more information on additional available spares, see the table,
QPix 420 Colony Picking System Replacement Parts on page 171.
Note: If fluorescent picking is required, you need to have a specific imaging
head based on fluorescent detection installed on the instrument. For more
information, contact technical support [email protected].
For information on performing a standard picking routine, see Conducting a
Picking Routine on page 65.
For information on performing a regional picking routine, see Conducting a
Regional Picking Routine on page 85.
Routines Window
The QPix 420 software allows you to run a new or existing routine using
various pre-configured routines from the Routines window.
Filter Pairs List
Note: Filter Pairs are available only if Fluorescent Imaging is installed. If the
Barcodes window does not display a filter pairs list, it means your System
has only White Light functionality installed.
If you have purchased the fluorescent imaging option, you can make imaging
adjustments with various supplied filter pairs using the Filter Pair list.
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Barcodes Window
The QPix 420 software lets you read barcodes in various ways.
Source barcodes can be listed in any order. The QPix 420 System searches the
list to validate that the source barcode is present. If it is not, a message
appears describing the erroneous receptacle.
Note: Validation barcodes are an option for source receptacles only. Barcodes
compatible with the barcode reader are code 39, code 93, and code 128.
Destination Options Window
Use the Destination Options window to configure your destination
microplate settings.
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Software Overview
Destination/Source Options Window (Regional Picking)
The Destination/Source Options window is configured especially for
regional picking. It will only appear when you are performing a regional pick.
Use it to control your regional picking source and destination deposit options.
Head/Sanitise Window
Choose head and sanitise options for your routine from the Head/Sanitise
window.
The top of the window allows you to select the relevant head for your routine.
The lower section of this window allows you to choose your sanitise options for
your routine from this section. The Sanitise Profile list displays all sanitise
profiles created using Manage Sanitise Profiles. Select the desired sanitise
profile and its related wash routine displays in the Wash Cycle table.
You cannot change sanitise profile settings from here. For information on how
to perform this task, see Creating and Editing Sanitise Profiles on page 61.
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Source Window
Use the Source window to choose your source Holder, Receptacle type, and
positioning, and picking depth.
The Settings Summary window displays a list of all settings configured for a
routine. This window will display different information based on the settings
you just made.
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Software Overview
Holder Layout Summary Window
The Holder Layout Summary window shows you how to correctly arrange
the microplate holders in the instrument for your routine dictated by the
selections made earlier. You must click the Checked? box to continue from
this window.
Test Image Window
Use the Test Image window to optimise your imaging settings for detecting
colonies.
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FL Test Image Window
A fluorescent test image is also created if you have chosen to perform
fluorescent imaging. This test image is similar to the standard white light test
image, but the only Acquisition settings for use are exposure and gain.
Feature Selection Window
Use the Feature Selection window to detect colonies you want to pick that
match a desired shape, size and proximity.
To perform both white light and fluorescent picking, toggle between the White
Light and fluorescent image tabs.
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Software Overview
Feature Counts Tab
The Feature Counts tab shows the number of feature counts detected on a
source receptacle. The barcode for the source receptacle is listed, the number
of features found is displayed, as well as the number of features to pick as
determined by the selection criteria.
Display Options Tab
The Display Options tab allows you to view additional information about the
receptacle image.
Note: This tab contains some Regional Picking specific options.
Load Plates Window
from this window.
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Control Plate Creation Processes
Use the Control Plate Creation process to create a batch of microplates
containing specified control samples. These can be created by picking colonies
from specified source receptacles into specified destination wells.
For information on conducting a control plate creation routine, see Control
Plate Creation Processes on page 107.
As with other processes, you must start with creating your routine.
Routines Window
For details of elements in the Routines windows, see Routines Window on
page 24.
Barcodes Window
The Control Plate Creation Barcodes window is simpler than the usual
Barcodes window. You have the option of choosing either Use Barcode
Reader or Generate Random Barcodes.
Destination Options Window
Use the Destination Options window to set your destination microplate
options. You can create up to 70 control microplates.
Note: If the stacker icons are greyed out and unselectable in the next
window, it is because you chose an unsuitable microplate in the current
window. The software knows the specifics of the stacker lane configuration for
your instrument, and allows you to choose only suitable microplates. Return
to this current window to select a suitable microplate.
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Software Overview
Head/Sanitise Window
The Head/Sanitise window allows you to choose a head and select a sanitise
profile. For more information on sanitise profiles, see Creating and Editing
Sanitise Profiles on page 61.
Source Window
The Source window allows you to configure your source holder and
receptacle, as well as set the picking depth into the agar.
Control Plate Window
The Control Plate window allows you to designate where the control samples
are placed on the destination receptacle.
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The Settings Summary window contains a full summary of the routine
settings you just configured.
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Software Overview
Holder Layout Summary Window
selections made at the Source/Destination step earlier. You must click the
Checked? box to continue from this window.
Test Image Window
The Test Image window is described in the Standard and Regional Picking
Processes section. For more information, see Test Image Window on page 28.
Feature Selection Window
The Feature Selection window is described in the Standard and Regional
Picking Processes section. For more information, see Feature Selection Window
on page 29.
Load Plates Window
from this window.
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Replication Processes
The QPix 420 software allows you to replicate your picked colony samples in
the following ways:
• Library Replication duplicates samples from one microplate to
another of the same format. You can create several copies of the
original microplate.
• Library Compression replicates samples from 96-well microplates to
384-well microplates. You can create several copies of the original
microplate.
• Library Expansion replicates samples from a 384-well microplate to a
96-well microplate. You can create several copies of the original
microplate.
All three tasks follow similar routine steps, so the differences only will be
highlighted. For information on conducting a replicating routine, For
information on performing a replicating routine, see Replication Processes on
page 123.
Routines Window
For details of elements in the Routines windows, see Routines Window on
page 24.
Barcodes Window
For details of elements in the Barcodes windows, see Barcodes Window on
page 25.
Microplates/Sanitise Window
Select your replicating source and destination microplates, dipping, stirring,
and copying options, and your sanitise profile from the Microplates/Sanitise
window.
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Software Overview
Head Window
The Head window allows you to set the head type and inoculation dipping
height options of both the source and destination microplate.
For information on the Holder Layout window, see Holder Layout Window on
page 22.
Load Plates Window
The Load Plates window displays the required layout and positioning for your
source, destination, and copy microplates (if you chose to make copies). You
must click the Checked? box to continue from this window.
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settings you just configured. You can print a copy of the settings by clicking
Print.
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Software Overview
Rearraying Processes
Rearraying allows you to re-deposit liquid samples between one or more
source and destination microplates. You can, therefore, consolidate chosen
wells into microplates in an ordered fashion.
For information on performing a rearraying routine, see Conducting a
Rearraying Routine on page 133.
As with other processes, you must start with creating your routine and
barcodes.
Routines Window
For details on routines, see Routines Window on page 24.
Barcodes Window
Use the Barcodes window to read barcodes in various ways.
Source Window
Use the Source window to rearray (transfer) selected colonies from existing
source receptacles into new destination receptacles.
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Destination Window
Use the Destination window to configure destination microplate settings.
Note: You cannot make a copy of a destination microplate during rearraying,
but you can make a copy within both picking and replicating processes.
Head and Sanitise Window
Choose head and sanitise options from the Head and Sanitise window.
The top of the window allows you to select the relevant head for your routine.
The lower section of this window allows you to choose your sanitise options for
your routine from this section. The Sanitise Profile list displays all sanitise
profiles created using Manage Sanitise Profiles. Select the desired sanitise
profile and its related wash routine displays in the Wash Cycle table.
You cannot change sanitise profile settings from here. For information on how
to perform this task, see Creating and Editing Sanitise Profiles on page 61.
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Software Overview
selections made at the Source/Destination step earlier. You must click the
Checked? box to continue from this window.
Load Plates Window
The Load Plates window displays the required layout and positioning for your
source, destination, and copy microplates (if you chose to make copies). You
must click the Checked? box to continue from this window.
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settings you just configured. You can print a copy of the settings by clicking
Print.
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41
Software Overview
Data Viewer Processes
The QPix 420 System allows you to view data and manage the data of previous
routines run on the instrument.
For information on performing a data viewer processes, see Data Viewer
Processes on page 159.
Data Viewer
The Data Viewer window allows you to search and view any previously-run
routine on the instrument. The routines are searchable in multiple ways, for
example by process or by tag, barcode, date, user, and location.
Database Management
In this window, Molecular Devices engineers or trained customers only can
update the database or perform an automatic backup of the database.
Note: Trained people only should perform this task.
The process also allows engineers and trained customer to set options for
backup and restore and versioning the software database.
You will need to run a versioning program following an install which also
contains a database upgrade.
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QPix Utility Processes can be run at any time and are an important part of the
ongoing maintenance of the QPix 420 System.
Manage Sanitise Profiles
Manage Sanitise Profiles allows you to set up various sanitise profiles as
required by various experimental needs. You will need to have at least one
sanitise profile created before you can successfully conduct a picking routine.
For more information on using sanitise profiles, see Creating and Editing
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Software Overview
Camera Alignment Process
To ensure the most accurate picking, the camera must be calibrated and
aligned correctly to achieve pin-to-spot accuracy, relating the image pixel coordinates with the instrument x and y coordinates. If the actuator is knocked,
picking accuracy might be affected.
Calibration and alignment are performed before the instrument is dispatched
and are checked by a Molecular Devices approved engineer during installation.
For more information on how to conduct camera alignment, see Aligning the
Camera on page 47.
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Instrument Utilities
Instrument Utilities allow you to perform the following maintenance and
cleaning activities.
Change Head
Change Head allows you to safely move the head of the instrument so you
can change it. For more information on changing the head, see Changing the
Head on page 48.
Pin Fire Test
Pin Fire Test allows you to fire all pins to ensure they are obstruction-free
before use. You can control the speed of the pin firing by moving the speed
slider at the bottom of the window. For more information how to conduct a pin
fire test, see Performing a Pin Fire Test on page 49.
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Software Overview
UV Sanitise Window
You can use the UV Sanitise window to sanitise the QPix 420 System interior
for a designated period of time (up to 600 seconds). For more information on
conducting a UV sanitise, see Conducting a UV Sanitise on page 60.
Sanitise
The Sanitise window allows you to wash the head outside of a routine (for
example, if the System had been unused for a long period of time). For more
information on conducting a sanitise, see Conducting a Sanitise on page 60.
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Instrument Maintenance
3
Molecular Devices® recommends regular and thorough maintenance of the
QPix 420 Colony Picking System to ensure it continues to function correctly.
The following maintenance tasks are available for the QPix 420 System:
• Aligning the Camera on page 47
• Changing the Head on page 48
• Performing a Pin Fire Test on page 49
For information on how to clean the instrument, see:
• Conducting a Sanitise on page 60
• Conducting a UV Sanitise on page 60
• Creating and Editing Sanitise Profiles on page 61
Aligning the Camera
To ensure the most accurate picking, the camera must be calibrated and
aligned correctly to achieve pin-to-spot accuracy, relating the image pixel coordinates with the instrument x and y coordinates.
1. From the Navigation window, double-click the Camera Alignment
Process icon. Ensure you are using a 96 pin head.
2. Place a QTray with agar onto the light table holder, and then click Next.
3. Click Goto Pos to move the head over the QTray.
4. Use the settings in the Acquisition section to sharpen and focus the
image you are working with.
5. Click Fire Pin A1 and, using the blue jogger arrows, jog the pin
down until it just touches the agar. You can adjust the increment for
each jog using the Dist (mm) field next to the arrows.
6. Click Retract Pin, and using the camera settings (Visit Position and
Set Position), align the camera to the hole in the agar.
7. Click Goto Camera and using the Vertical blue jogger arrows, zoom
into the hole in the agar. Adjust camera settings as necessary.
8. Using the Lateral red and green jogger arrows, jog the camera until
the centre of the hole aligns with the red crosshairs. You can adjust the
increment for each jog using the Move Size list.
9. Click Set when you are satisfied with your camera alignment settings.
10. Click Next to complete this process.
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47
Changing the Head
To remove the head from the instrument, Molecular Devices recommends you use
the QPix 420 software to help you safely perform this task.
1. From the Navigation window, double-click Instrument Utilities, and then
double-click the Change Head icon. The Change Head window appears.
WARNING! If moving head manually, use handle to avoid pinching.
1. Select one of the following:
 Change Head allows you to safely move and change the head.
 Park Head allows you to home the head to its starting location.
A warning message appears, telling you to ensure the bed is clear.
2. Click OK.
If you clicked Park Head, the head homes to its starting location and the
process is complete.
If you clicked Change Head, the head moves to the front of the
instrument. You can now safely remove the head.
3. To remove the head, unscrew and remove the thumbscrew, which secures
the head to the actuator assembly, taking care not to lose the washer. Be
careful not to touch the camera.
4. Grab the head handle and slide it out of the actuator.
5. If you have finished using the head, slide it into the metal cover (pins
facing inwards) and securing it in place with the thumbscrew.
6. Click Next to return to the Instrument Utilities window.
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Performing a Pin Fire Test
The Pin Fire Test checks that pins are obstruction-free and can move freely.
1. From the Navigation window, double-click Instrument Utilities, and
then double-click the Pin Fire Test icon.
The Pin Fire Test dialog opens stating that once you click OK, the head
will move to the Change Head position.
2. Click OK.
The Pin Fire Test window appears.
3. Select the various parameters for your test from the following options:
 Select Head allows you to select the head to be tested.
 No of rows displays the number of rows of pins on the head.
 No of columns displays the number of columns on the head.
 Fire Pins In Sequence test fires the pins in the order you select
from the following check boxes (default is by column order). This
test continues until you click Stop or all the pins have been fired.
 X Row First fires the pins one by one in row order.
 Rearray Valve activates pin dampening as they retract.
 Fire All Pins test fires all the pins at once.
 Fire Pins Randomly randomly test fires the pins. The pin map
shows which pins are firing by temporarily changing the colour of
the fired pin. This test continues until you click Stop or all the pins
have been fired.
Click Next. The Pin Fire Test dialog opens, telling you to move the
head to a safe parking position.
4. Click OK to start the test.
CAUTION! Wait for all firing to stop before opening the door.
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49
50
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Instrument Overview
4
Introduction
The QPix 420 Colony Picking System is constructed within a welded steel
framework. All working parts are located within the interior of the instrument.
Before operating the instrument or performing maintenance operations, make
sure that you are familiar with the safety information in this user guide. For
more information on safety, see Safety Information on page 9.
The door on the front of the instrument, is fitted with an electro-mechanical
lock, allowing it to operate only when the door is correctly closed and locked.
The bed of the instrument contains source and destination plate holders, and
wash baths, making it easier to clean pins both before and during routines.
For more information on cleaning and preparing the instrument, see
Preparations for Running a Routine on page 59.
For more information on regular instrument maintenance, see Instrument
Maintenance on page 47.
Pre-Power-Up Checklist
1. Check the Emergency Stop button (see Figure 4-2 on page 54) is
pulled out. The instrument will not start if the button is pushed in.
2. Confirm the instrument bed is clear of obstructions and loose items.
3. Confirm that all motor tracks are free of obstruction.
4. Confirm there are no obstructions to movement of the head.
Power-Up Procedures
1. Turn on the power supply to the compressor.
2. Push the Start button on the front panel (see Figure 4-2 on page 54).
The Power On icon displays on the front panel. If the power to the
QPix 420 System does not turn on, it is likely that the door is open or
the Emergency Stop button is pushed in (see Figure 4-2 on page 54).
The instrument cycles through various processes which is indicated in
the LCD Indicator panel. When initialization is complete, this message
will disappear, and the display icons will appear. For more information
about display icons, see Display Icons for QPix 400 Series of Colony
Picking Instruments on page 55.
3. Check that the Air Pressure OK icon on front panel is displayed.
4. Switch on the computer and wait for it to discover the QPix 420 Colony
Picking System local network.
Note: A common mistake at this point, is trying to launch the software
before the network has been discovered. If this happens, an error
message will appear, notifying you that it cannot find the instrument.
5. Once you are certain the computer has finished its initialization, from
the Desktop, double-click the QPix 420 Colony Picking System icon.
Every time the instrument is used, the three axes will sequentially run
through their “Initialize drives” routine. This enables the drives to find
their respective home positions. The QPix 420 System must be allowed
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Instrument Overview
to complete this routine without interference to ensure that there is no
damage to the instrument or its ancillary equipment.
Shutdown procedure
1. Click Exit from the File menu in the Navigation window. The QPix 420
System closes down.
2. Click Start at the bottom of your computer screen, and then click Shut
Down. Wait for the computer to switch off completely.
3. Switch off the instrument by pushing the STOP button on the front
panel.
4. Switch off the power at the mains.
Installation
Installation is to be undertaken only by Molecular Devices® approved
personnel. The QPix 420 System must be located in a well ventilated area. For
more information on installation, see Technical Specifications on page 173.
Mounting the Instrument
Be sure to install the instrument on a suitably strong and firm surface.
Because of the weight of the instrument and the movement of the head during
most processes, some vibration and wobble can occur. This can reduce
performance effectiveness, most notably a reduction in the quality of imaging
results.
Molecular Devices supplies a suitable table for purchase, but if you choose to
not purchase this table, be sure that the table on which you mount the
instrument is stable enough to minimize vibration and wobble.
Note: The instrument is supplied with four adjustable leveling feet.
Once the instrument is mounted on a table, be sure to adjust these feet
accordingly in order to maximize performance.
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Instrument Layout
3
2
1
Figure 4-1: Angled Front View Showing a Three-Holder Layout
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Item
Description
1
Plate Holders
2
Imaging Table with Source Tray loaded
3
Wash Baths
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Instrument Overview
Front Panel Display
1
2
4
3
Figure 4-2: The QPix 420 System Front Panel Display
Item
54
Description
1
LCD Indicator Panel
2
START Button
3
STOP Button
4
Emergency Stop Button
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Display Icons
1
2
3
5
4
6
Figure 4-3: Display Icons for QPix 400 Series of Colony Picking Instruments
Item
Description
1
Power is on
2
Air pressure is low
3
Air pressure is correct
4
The instrument is running a process (not applicable for
Instrument Utilities).
5
The interior light is switched on
6
The UV light is switched on
Service and Maintenance
You are responsible for day-to-day maintenance, details of which are explained
in the following pages.
In addition, Molecular Devices strongly recommends that a complete
instrument maintenance be carried out every 6 months by a Molecular Devices
approved service engineer. Maintenance contracts or one-off visits can be
obtained from your regional Molecular Devices office.
For more information on service and maintenance processes, see Instrument
Maintenance on page 47.
General Maintenance
1. Ensure that the QPix 420 System interior is free from dirt and dust (for
more information on cleaning, see Cleaning Procedures on page 56). In
particular, check the surface of the x-axis drag-chain support bracket.
Dust and debris accumulated here can be swept onto the QPix 420
System bed during operation.
2. Remove, clean, and sanitise wash bath(s) and brushes.
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Instrument Overview
3. Check the air regulator for signs of moisture. If necessary, twist the
drain clockwise approximately half a turn to force moisture out. Some
types of regulator might require the drain purge to be pushed up
towards the regulator bowl.
Weekly Maintenance
1. Dismantle head completely and thoroughly clean all component parts.
2. Check operation of the Emergency Stop button.
3. If the QPix 420 System door shows any signs of damage you need to
request a replacement door from Molecular Devices.
Bi-annual Maintenance
Maintenance performed by Molecular Devices approved personnel.
Cleaning Procedures
Cleaning the Instrument Interior
For efficient decontamination of pathogenic micro-organisms, all nonremovable parts within the QPix 420 System should be wiped with a cloth
using 70% ethanol.
Abrasive cleaners should not be used, as they will damage the surface of the
bed.
The QPix 420 System can be left in a laboratory during formaldehyde vapor
fumigation at an appropriate concentration.
For more information on cleaning, see Preparing your Wash Baths on page 59,
Conducting a Sanitise on page 60 and Conducting a UV Sanitise on page 60.
Note: Excessive formaldehyde treatment will damage sensitive electrical and
optical components.
Note: To avoid damaging the instrument or any of its components, if a
solution spill occurs in the instrument interior, especially if it is 1% sodium
hypochlorite (bleach), be sure to conduct an immediate clean up using your
standard cleaning practices.
Incoming Compressed Air Supply
Compressed air is required for the picking action of the picking pins. The oilfree compressed air unit draws air from the local environment and delivers it
to the instrument through the regulator set to 100 psi.
Automated Pin Cleaning
The reusable picking pins are subject to repeated pin cleaning during a
routine. Specifically, they are cleaned prior to the first pick, between each
cycle of picking, and at the end of the run. The cleaning routine consists of the
following configurable tasks:
• Brushing of the pins in the three baths.
• Halogen dryer heats the picking pins and removes residual ethanol.
•
Note: Automated cleaning should not replace the sanitisation of picking pins
by sonication.
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Removable Parts
You can clean and remove all parts of the QPix 420 System components that
come into close contact with biological materials.
Note: Molecular Devices recommends you always use ethanol for cleaning,
because autoclaving is not compatible with anodized parts.
The Head
The Z ball-screw drive carries a unique actuator System that accommodates
the head. This allows for easy exchange and set-up of the head.
Although it is possible to move the head manually, Molecular Devices
recommends using the QPix 420 System to safely remove the head. For more
information on removing the head, see Changing the Head on page 48.
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Instrument Overview
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Preparations for Running a Routine
5
Molecular Devices® recommends regular and thorough preparation of the QPix
420 Colony Picking System to ensure it continues to function correctly.
This chapter describes the preparation of the instrument you should conduct
before running any routine.
Before starting any new routine, Molecular Devices recommends you perform
a manual clean (using 70% ethanol) and UV sanitise of the interior of the
instrument. For more information, see Conducting a UV Sanitise on page 60.
It is also important that the sanitise profiles are edited prior to starting a new
routine. For more information, see Creating and Editing Sanitise Profiles on
page 61.
Preparing your Wash Baths
The QPix 420 System contains three wash baths which you will use when
running various routines. It is important that these baths are filled with a
suitable amount of solutions and they are arranged correctly.
For a typical picking routine, Molecular Devices recommends the following
solutions are put in the following wash baths:
• Wash Bath 1 (furthest from front) - 70% ethanol
• Wash Bath 2 (middle wash bath) - sterile water
• Wash Bath 3 (closest to the front) - 1% sodium hypochlorite (bleach)
For other routines, follow their relevant designated procedures.
Note: Bleach can cause corrosion if left in the instrument for too long. It
should be removed from the instrument immediately after use. Bleach is
typically required for difficult-to-sterilise organisms, such as yeast and
Streptomyces.
Note: Be sure to validate the wash baths and cycles that are required for
their application.
Note: Before starting any sanitise routine, remove loose items from the
interior of the instrument.
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59
Conducting a Sanitise
1. In the Navigation window, double-click Instrument Utilities, and then
double-click Sanitise.
2. From the Sanitise window, select a Sanitise Profile from the list and
select a Wash Cycle tab.
Note: If you want a different wash cycle to what is available, you will
need to cancel this routine and create a new sanitise profile. For more
information, see Creating and Editing Sanitise Profiles on page 61.
3. Click Wash. The System will run the displayed wash cycle.
4. Click Next to return to the Navigation window.
Conducting a UV Sanitise
1. In the Navigation window, double-click Instrument Utilities, and then
double-click UV Sanitise.
2. From the UV Sanitise window, either accept the default (600 seconds)
or change the duration of the sanitise in the Duration of Ultra Violet
Exposure field.
3. Click Begin. The UV light switches on for the assigned time (unless you
get an error message, which will state the problem). When the sanitise
is complete the light goes out, and a Completed message appears
above the Begin button.
After the routine starts, stop the UV sanitise any time by clicking Stop.
Note: As a final step, remember to top up your wash baths with
relevant cleaning fluids and wipe down the surfaces of the interior.
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Creating and Editing Sanitise Profiles
The QPix 420 Colony Picking Software comes with one default sanitise profiles.
If this is the first time performing any routine, Molecular Devices recommends
you open Manage Sanitise Profiles to edit the supplied default profile to suit
your specific needs.
Sanitise profiles consists of two types of wash cycles - Multi Stage and Single
Stage. Wash cycles can contain any number of wash bath steps, all of which
have to be created in the Manage Sanitise Profiles window.
Note: You cannot edit sanitise profiles when running a routine, so while you
are working in the Manage Sanitise Profiles window, it is worth creating a
range of various profiles that you think you might need for future routines.
1. In the Navigation window, double-click the Manage Sanitise Profiles
icon. The Manage Sanitise Profiles window appears.
2. In the Manage Sanitise Profiles window, click New.
To edit a profile, skip to Editing a Sanitise Profile on page 62.
To delete a profile, skip to Deleting a Sanitise Profile on page 63.
3. In the Add Profile dialog, type the profile name in the Name field and
then select one of the following options for your wash profile:
Single Stage means you plan to use the same wash cycle before and
during a routine.
Multi Stage means you want different wash cycles before and during a
routine.
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4. Click Add. The sanitise profile now appears in the Profiles table along
with all other sanitise profiles.
Although you have created a sanitise profile, it needs at least one wash
bath step to make it useful in a routine.
5. To add wash bath steps to a sanitise profile, in the Manage Sanitise
Profile window, click Edit.
Editing a Sanitise Profile
1. From the Profiles table, highlight a sanitise profile, then select one of
the following wash cycle options from the Stages list:
First and Main Wash Cycle (displays only if you selected Single
Stage in the Add New Profile dialog) creates one wash cycle to be
used both before and during a routine.
First Wash Cycle creates the pre-routine wash cycle of a Multi Stage
sanitise profile.
Main Wash Cycle creates the wash cycle to be used during the routine
of a Multi Stage sanitise profile.
2. Click Edit. This activates the Add and Remove buttons related to each
wash bath step in the Steps table, and deactivates all other buttons.
3. From the Bath Name list, select a wash bath (1, 2 or 3), and then
type relevant amounts into the following fields:
Bath Cycles sets the number of times to wash pins in that wash bath.
Dry Time (seconds) sets the number of seconds for the pins to be
dried in the halogen dryer.
Wait After Drying (seconds) sets the number of seconds you want to
wait before continuing.
4. Click Add if you want to add another wash bath step to the wash cycle.
5. Click Remove if you want to remove an existing wash bath step.
6. Repeat the previous steps until you have created all wash bath steps
you want to associate with this wash cycle.
7. Click Save. This sanitise profile is now available for all processes.
8. If you are creating a sanitise profile with Multi Stage cycles, select the
other wash cycle from the Stages list and repeat the previous steps.
9. When you have finished adding wash bath steps to your wash cycles,
Click Next to return to the Navigation window.
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Note: Now you have edited at least one sanitise profile, as you
prepare the instrument for a routine, remember to install correct
cleaning fluids in the correct number of wash baths.
Deleting a Sanitise Profile
1. In the Manage Sanitise Profiles window, select a profile, and then
click Delete. A confirmation dialog appears.
2. Click Yes. The profile is removed from the Profiles table.
Now that you have edited at least one sanitise profile, you can perform the
following routines:
• Conducting a Picking Routine on page 65
• Conducting a Regional Picking Routine on page 85
• Replication Processes on page 123
• Running a Rearraying Routine on page 138
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Conducting a Picking Routine
6
The QPix 420 Colony Picking Software allows you to pick colonies from
receptacles using either the standard or regional process. Both processes have
white light and fluorescent picking capabilities.
Note: If you want fluorescent picking on your instrument, the QPix 420
Colony Picking System must be configured with a specific fluorescent imaging
head. For more information, contact technical support at
[email protected].
Note: If you have the fluorescence imaging module, a picking routine just
using white light imaging will take longer because more images are taken.
This chapter contains the following sections:
• Preparing for a Picking Routine on page 65
• Creating and Editing a Picking Routine on page 66
• Running a Picking Routine on page 74
Preparing for a Picking Routine
You need to perform some preliminary steps before successfully conducting a
picking routine. For more information on these steps, see Preparations for
Running a Routine on page 59.
If this is your first picking routine on the QPix 420 System, you must edit the
supplied sanitise profile to suit your needs. For more information on sanitise
profiles, see Creating and Editing Sanitise Profiles on page 61.
If you have made any adjustments to the instrument, such as changing the
head, you will have to align the camera again. For more information on camera
alignment, see Aligning the Camera on page 47.
Before you begin any new picking routine, Molecular Devices® recommends
you perform a sanitise, UV sanitise, and a manual clean of the interior of the
instrument with ethanol. For more information on these tasks:
• See Conducting a Sanitise on page 60.
• See Conducting a UV Sanitise on page 60.
Remove any loose items from the interior of the instrument and remember to
top up your wash baths with relevant cleaning fluids.
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Creating and Editing a Picking Routine
Now that you have created and edited at least one sanitise profile, performed
both sanitise routines, and given the instrument interior a manual clean, you
are ready to create a picking routine. This consists of the following steps:
• Selecting Barcode Reading Options on page 67
• Setting Filter Pairs (Fluorescent Light only) on page 69
• Setting Destination Options on page 69
• Selecting Head and Sanitise Options on page 71
• Setting your Picking Source on page 72
• Viewing the Settings Summary on page 73
Note: Not all steps in this chapter will be available on your instrument. This
will depend on which additional features you purchased. Optional features will
be identified as appropriate.
1. In the Navigation window, double-click the Picking icon.
2. In the Picking window, click Picking Type and select one of the
following:
 White Light indicates you want to use only white light to illuminate
and identify colonies to pick.
 White Light And Fluorescent (optional feature) indicates you
want white light to illuminate and identify colonies, and fluorescent
light for determining the desired colonies to pick.
3. Click Apply, and then click Start.
The System “homes” the drives, and then the Routines window opens.
This allows you to create or edit existing routines.
4. In the Routines window select New Routine, and then click Next.
To run an existing routine, select Run Existing Routine. This saves
you time by allowing you to choose an existing routine from the Select
Routine list and either editing it, or using it in its exact configuration
(Select Skip Steps for this option).
 Select Skip Steps if you want to keep all existing parameters for
the routine and skip directly to the Settings Summary window.
Delete routines from the Select Routine list by clicking Delete.
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If you selected White Light earlier, the Barcodes window appears.
If you selected White Light and Fluorescent The Filter Pair and
Barcodes window appears.
Selecting Barcode Reading Options
The Barcodes window allows you to select barcode reading options.
The Filter Pair and Barcodes window allows you to select filter pair and
barcode reading options. For more information on filter pairs, see Setting Filter
Pairs (Fluorescent Light only) on page 69.
Note: Molecular Devices recommends you always use barcodes for accurate
data tracking.
Note: If you choose to create validation or manual barcodes they will only be
applied to your source microplates.
1. If using the barcode reader, leave the Use Barcode Reader check box
selected (default), and then select a Read Failure Action option.
Use Barcode Reader means the barcode reader will automatically
scan receptacles for barcodes (both source and destination).
2. Select one of the following options from the Read Failure Action
section, in case a barcode cannot be read correctly:
 Manual prompt launches a dialog where you can manually type a
barcode or microplate name (both source and destination
receptacles).
 Skip Receptacle tells the instrument to cease looking for a
barcode and look for a barcode on the next receptacle (both source
and destination receptacles).
Note: If the instrument fails to identify a barcode for the source
receptacle, the routine will end, as the source needs a valid barcode.
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3. Enter your full range of barcodes for this routine in the Validation
Barcode table using the following options.
This helps you to check barcodes on source receptacles as they are
scanned by the barcode reader. You can list the barcodes in any order.
The instrument scans the Validation Barcode list to confirm the
source barcode is present. If it is missing, a message appears
describing the erroneous receptacle.
 Insert means you need to type each bar code manually into the
Insert field, and then click Insert.
 Import means you can import barcodes from a text or .csv file.
 From Database means you can import barcodes from a database.
4. If you are not using barcodes, and you have cleared the Use Barcode
Reader check box, select one of the following:
Generate Random Barcodes generates a random and unique
barcode for every receptacle used (both source and destination), with
prefix Auto. This option prohibits manually typing barcodes.
Clicking the Generate List button, allows you to create your own
receptacle identifiers. The Generate Barcode List window opens.
Type relevant information into the following fields:
 Prefix creates a text label for your microplate identifiers.
 Start Number sets the starting identifier number.
 Digit Padding adds zeros before the identifier number.
 Number to Generate sets amount of identifiers for this routine.
To preview your manually generated barcodes, click Generate. A list of
these barcodes displays in the Manual Barcodes table.
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5. After choosing your barcode reading option, click Next.
The Destination Options window opens. For more information, see
Setting Destination Options on page 69.
Setting Filter Pairs (Fluorescent Light only)
If you have selected the fluorescent light option, the Filter Pair Selection
feature is contained within the Barcodes window. In this case, the window is
called Filter Pair And Barcodes.
1. Choose a suitable filter pair from the Filter Pair list.
2. After you have selected your filter pair for this routine, click Next.
The Destination Options window appears.
Setting Destination Options
The Destination Options window allows you to configure your destination
Setting your Picking Source
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1. In the Destination Options window, choose a destination microplate
from the Select Destination Microplate list. If you do not see a
microplate that you use on this list, please contact Molecular Devices to
see if we can add it to the list.
2. Choose from the following additional options:
 Multi Dip indicates you want the instrument to dip the pins into the
receptacle multiple times per dip.
 Number of Dips tells the instrument how many dips per deposit
you want it to make.
 Stir Destination stirs the pins in the destination receptacle wells.
If you choose this option, you cannot multi-dip.
3. Click Make Copy if you want to create a copy of the destination
microplate. If you choose this option, you must also select the other
destination microplate to copy using the Select Copy Microplate list.
4. Choose between By Columns or By Rows as the Deposit Order for
the destination microplate.
5. Decide your Deposit Strategy between the following options:
 Fill All Microplates tells the instrument to fill every well of the
destination microplates.
 New Microplate For Each Position indicates one QTray or Petri
dish is considered one position. Clicking this means a new
destination microplate will be used when picking begins in a new
position.
 New Microplate For Each Batch indicates two omni trays are
considered as one batch. Clicking this means a new destination
microplate will be used when a new batch of source microplates are
loaded onto the System bed.
6. To edit the Destination Microplate Template, click Edit. This
template allows you to clear various wells so that they are not picked,
for example when control wells are desired. The Edit Destination
Microplate Template dialog appears.
Cleared wells are displayed in light blue and selected wells are pink.
7. Click any well you want to leave empty, and right-click and drag your
mouse over multiple wells you want to remain empty. Click a well again
to re-select it.
8. Click Exit, and then click Next. The Head/Sanitise window appears.
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Selecting Head and Sanitise Options
1. In the Head/Sanitise window, choose from the following Picking
Head Options:
 Picking Head allows you to choose various short or long heads.
 Pin Columns Before Inoculation allows you to set the number of
pins available to pick with before inoculation into the destination
microplate. This helps inoculate colonies faster into the destination
microplate (without having to wait until all pins have been used).
 Wash between Partial Inoculation allows you to wash pins
between shorter inoculations.
Note: In the Destination Options window, if you selected By Rows
earlier, you can select 1 to 7 rows, and if you selected By Columns,
you can select 1 to 11 columns.
2. Use the Inoculation Heights (mm above well bottom) fields to set
the depth (in millimeters) the pin travels to above the bottom of a well
for both your Destination and Copy receptacles. The Copy field
appears here if you chose Make Copy in the Destination Options
window. Default values are displayed for each microplate type chosen
earlier.
3. Select a sanitise profile from the Sanitise Profile list.
Note: If none of the sanitise profiles suit your routine, you will need to
exit the routine at this point and create a sanitise profile. For more
4. Click Next. The Source window appears.
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Setting your Picking Source
The Source window allows you to configure your picking source microplate.
1. In the Source window, choose your source holder, receptacle type and
positioning, and picking depth.



Holder selects the source plate holder layout. When using QTrays,
this is the default.
Receptacle displays possible receptacles for the holder selected.
Positions describes receptacle quantity and displays their
positions. For example two QTrays.
Note: When using Validation barcodes, if you are using only one
source barcode, one source receptacle position will only display here.
Also, the positions number is automatically greyed out. For more
information, see Selecting Barcode Reading Options on page 67.


Picking Depth Into Agar (mm) sets the travel depth for the
picking pin into the agar in the source tray.
Limit Max. Number Of Features Per Position limits the number
of colonies (Features) per Position (QTray or Petri dish). If you
select this, the Max. Number Of Features Per Position check
box becomes editable.
Note: Selecting this option makes it impossible to change this number
in the Feature Selection section. The number per region will be set
and cannot be changed. For more information on limiting features per
position, see Selecting Colonies on page 78.
2. Click Next. The Settings Summary window appears.
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Viewing the Settings Summary
The Settings Summary window contains a full summary of the picking
routine settings you just configured.
Print a copy of the settings by clicking Print, or click Next to continue.
The Holder Layout Summary window appears.
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Running a Picking Routine
Now that you have configured your parameters, you are ready to prepare the
instrument and run the routine. This consists of the following steps:
• Arranging the Layout of the Holders on page 74
• Creating a White Light Test Image on page 75
• Creating a Fluorescent Test Image (Fluorescent light only) on page 77
• Selecting Colonies on page 78
• Viewing a Summary of Selected Colonies on page 80
• Viewing Additional Display Options on page 81
• Continuing or Saving Your Routine on page 81
• Loading the Plate Holders on page 82
• Viewing the Picking Progress on page 82
• Completing or Running Another Routine on page 83
Arranging the Layout of the Holders
The Holder Layout Summary window shows you how to correctly
arrange the microplate holders in the instrument for your picking
routine. This is defined by the selections you made earlier in this
routine.
1. Follow the holder layout instructions on the screen, and after you are
certain you have loaded everything correctly, click Checked?
If you do not select Checked? you cannot continue the process.
Note: The instrument door now locks. The only way to over-ride this is
to click Cancel or press the Stop button on the front of the instrument.
Note: After clicking Next here, you can no longer click Back.
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2. Click Next. The Please load source window appears.
3. After you have loaded the source tray in its correct location, click Next.
The instrument now takes a white light test image of the source tray.
The Test Image window appears.
Creating a White Light Test Image
The Test Image window contains the test image and an image adjustment
pane. Use these settings to optimize white light settings for picking colonies.
Note: When you are also conducting fluorescent imaging, this window is
labelled WL Test Image in the left menu column to distinguish between the
white light and fluorescent test images.
As well as detecting desired colonies, you can also discard debris or detected
objects that are not colonies from here.
1. Adjust Acquisition, Detection, and Remove Debris settings here.
 The Receptacle list displays the number of source receptacles to
view.
2. In the Acquisition section, adjust the following. To apply these
settings, you must click Grab Image.
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Exposure (ms) allows you to control the amount of light exposed
to the sample (10ms to 1000ms).
 Gain allows you to increase the image signal without increasing the
amount of light exposed to the sample.
3. In the Detection section, adjust the following:
Use Auto Thresholding automatically detects colonies (check box is
selected as a default). Deselect this check box to manually edit these
settings and move the slider to the position where all the desired
colonies are colored green.
4. In the Display section, view three different images to detect colonies.
To change views, select one of the following from the Display list:
 Image And Overlay displays both green threshold color and
yellow rings for detected colonies.
 Image Only displays only the yellow rings. No threshold green is
displayed.
 Overlay Only displays only a black and white image of the
detected colonies with yellow detection rings.

Figure 6-1: Various Image Types based on Display List Selection
5. In the Remove Debris section, adjust the following. Use these settings
to discard detected debris from the images. When excluding debris, any
object that is excluded will not have the yellow line circling the detected
object.
 Diameter (mm) discards detected objects smaller than the defined
measurement.
 Axis Ratio discards detected objects smaller than the defined
measurement (in a percentage).
Note: When discarding debris, be sure to discard only debris smaller
than the desired colonies, otherwise this will affect the detection of
colonies and what you can pick. Excluding larger colonies will be
explained in the next step.
Features Found displays the number of features (colonies)
detected after excluding the debris. This dynamically updates with
your changes.
6. Click Next. The System begins “Imaging and Image Processing.” After
the imaging, the Feature Selection window appears.

Note: If you selected White Light and Fluorescent at the start of
this routine, clicking Next here starts the fluorescent imaging.
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Creating a Fluorescent Test Image (Fluorescent light only)
The Fluorescent Test Image window contains the test image and an imaging
adjustment pane.
Use these settings to optimize fluorescent light settings for picking colonies.
1. Under the Acquisition section, adjust the following:
 Exposure (ms) allows you to control the amount of light exposed
2. Click Grab Image to save your settings.
3. Click Next.
The System begins “Imaging and Image Processing.” After the image
processing is completed, the Feature Selection window appears.
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Selecting Colonies
When the imaging is completed, the Feature Selection window appears,
allowing you to pick colonies of a desired shape, size and proximity.
Note: If your routine consists of both fluorescent and white light imaging, the
Feature Selection window will contain two tabs. Toggle between the two to
select colonies.
The source receptacle with its detected colonies displays in the center and the
barcode for that receptacle is displayed to the right.
Pickable colonies display in yellow, while unpickable colonies (those that are too
close to the edge of the receptacle or do not match your selection criteria) are
displayed in red.
Any colony not circled has been excluded from the selection either at the test
image stage, or because it was discarded using the remove debris settings.
If you are performing both fluorescent and white light imaging, the Feature
Selection window contains the following tabs:
• White Light displays everything captured using white light.
• Fluorescent Filter Pair Name (Fluorescent light only) displays
everything captured with the filter pair chosen earlier.
Toggle between the tabs to select colonies.
1. In the Feature Selection window, use the slider bars beneath the
imaged source receptacle to zoom in for a closer look at the colonies or
adjust the image contrast as required.
2. In the Selection section, adjust the following parameters to control and
optimize the size and shape of desired colonies as well as exclude those
colonies that are too close together:
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


Compactness sets the level of irregularity for picking colonies. The
value is a ratio of the perimeter divided by the area of the colony, so
irregular shaped colonies will be closer to 0 and regular shaped
colonies will be closer to 1. The System default value is that any
colony equal to or less than 0.65 and will not be picked.
Axis Ratio measures how oval the colony is. The value is a ratio of
the longest diameter divided by the shortest diameter, so oval
shaped colonies will be closer to 0 and round colonies will be closer
to 1. The System default value is that any colony equal to or less
than 0.65 will not be picked.
Min Diameter (mm) sets the minimum diameter of colonies for
picking. Any colony equal to or smaller than the value stated in the
adjacent field will not be picked.
Note: Min Diameter (mm) cannot be lower than the diameter value
set in the Debris Discard section of Test Image.
Max Diameter (mm) sets the maximum diameter of colonies for
picking. Any colony equal to or greater than the value stated in the
 Min Proximity (mm) sets the distance between colonies to be
picked, so that when picking one colony another adjacent colony
will not be picked. The System default value is 0.45mm.
3. If required, manually select your desired colonies by right clicking on
them, and either picking or discarding them, as shown in the following
image:

4. View details of any displayed colony by holding your cursor over that
colony. Properties of that colony display in a popup. If a colony has not
been selected, the reason for this will be highlighted in red.
5. (Fluorescent imaging only) Adjust the histogram to obtain the
optimal selection of colonies.
The Histogram displays the level of colony intensity within a selected
image. The peaks show the distribution of the intensity of the colonies.
6. Set intensity measurements with the following settings:
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Mean Intensity is the average fluorescence of the detected colony
(the fluorescence of all the pixels within the colony perimeter
divided by the number of pixels within the colony perimeter).
 Median Intensity is the middle fluorescence value of all the pixels
within the detected colony perimeter.
 Geometric Intensity is the geometric intensity of the detect
colony (the fluorescence of all the pixels with the colony perimeter).
 Centre Mean Intensity is the average fluorescence value of the
middle 9 pixels within the detected colony perimeter.
7. Adjust your colony totals with the following settings:

Total Feature Count is the total features available to pick based
on your criteria. This number resets as you adjust these criteria.
 Limit Colonies limits the total number of pickable colonies. If
Limit Max. Number of Feature Per Region was selected in the
Setting your Picking Source section, this option will be grayed out
and the total number of colonies for picking will display. You cannot
change this number.
8. Click the Export Image button to save the image in any of the
following formats: .bmp, .jpg, or .png file.

The Feature Counts tab shows the number of colonies detected on a source
receptacle. The barcode (identifier) for the source receptacle is displayed,
along with the number of found colonies, as well as the number of colonies to
pick as determined by the selection criteria.
1. Click the Feature Counts tab to view a summary of pick information.
2. Export colony data to a .csv file by right-clicking in the table and
selecting Export.
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Viewing Additional Display Options
source receptacle image.
1. Click the Display Options tab to adjust the display options of the
colony selection.
Display Detected Features displays all detected colonies with a
yellow circle when the check box is selected. When not selected,
detected features are not displayed (selected by default).
 Shade Features gives the detected colonies some shading for
clearer visualization. (cleared by default).
 Display Proximity Indicators displays connecting red lines
between one detected colony to its closest neighbor.
Shade Exclusion Zone creates an exclusion zone (red shading on the
image) where the System is not able to pick. When not selected, the
red hatching is removed from the image (selected by default).
After you have made all your feature selections and adjustments, you
are almost ready to begin your picking routine.
2. Click Next. The Continue Or Save New Routine dialog appears.
Continuing or Saving Your Routine
1. In the Continue or Save New Routine dialog, choose one of the
following:
 Routine Without Saving means you do not want to save the
settings for this routine for future use.
 Save Routine means you want to save the settings for this routine.
2. To continue the routine without saving, click OK.
To save this routine, select Save Routine, type a name in the Name
field, and then click Save.
The Load Plates window appears.
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Loading the Plate Holders
need to load for your picking routine.
1. Based on the layout of the plate holders shown in the Arranging the
Layout of the Holders section, load the plate holders with the correct
destination microplates (numbers 1 through 12).
2. In the Load Plates window, after you are satisfied you have loaded the
plate holders correctly and complied with all items in the onscreen
checklist, click Checked?
3. Click Next. The Please load
4. The picking routine begins, and the Picking Progress window
appears.
Viewing the Picking Progress
The Picking Progress window displays a summary of this picking routine,
including a timeline to tell you how long to completion.
The Picking Progress window displays the following information:
•
•
•
82
Start Time shows the time the picking of the colonies began.
Source Barcode shows the barcode of the source receptacle being
picked from.
Pin is the picking pin being used.
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•
•
•
•
•
•
•
•
Copy Plate No is the barcode of the copy receptacle that is being
picked into (if selected in the setup).
Destination Barcode is the barcode of the destination receptacle that
is currently being picked into.
Destination Offset is the well into which the pins will be lowered. This
will change if using a 384 well microplate.
Colonies Picked is the number of colonies picked so far.
Colonies To Pick is the total number of colonies to be picked.
Estimated Time Remaining indicates remaining time.
Current Action displays the current action of the System, for example
Pick, when the System is picking.
Pause allows you to safely pause the routine.
Completing or Running Another Routine
When all source micropates have been loaded, the routine is complete. At this
point, the Finished Picking Current Batch dialog appears.
1. In the Finished Picking Current Batch dialog, select one of the
following options:
 Finish Picking ends this picking routine.
 Continue With Image Review allows you to review and edit the
colony selection settings again before running the same routine
with another source tray.
 Continue Without Image Review allows you to run the same
routine again with a difference source tray, but without reviewing
and editing colony selection settings.
2. Click OK.
 If you selected Finish Picking, the Picking Summary window
appears. Export the picking data for this routine by clicking Export.
 If you selected Continue With Image Review, the Test Image
window appears. See Creating a White Light Test Image on page 75
and Creating a Fluorescent Test Image (Fluorescent light only) on
page 77 for a reminder of the necessary steps.
 If you selected Continue Without Image Review, the Please
load source dialog appears. See Running a Picking Routine on
After all picking routines are completed, the Picking Summary dialog
appears, showing the number of source colonies picked, along with the
number of destination microplates used, and any missing source
receptacles.
You can export this information into a table by clicking Export.
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3. Click Next. The Process Completed window appears.
4. Click Finish to return to the Navigation window.
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Conducting a Regional Picking Routine
7
The QPix 420 Colony Picking Software allows you to pick colonies from
receptacles using either the standard or regional process. Both processes have
white light and fluorescent picking capabilities.
There are some additional viewing and selection options with a regional picking
routine compared to standard picking. For more information on regional
feature selection, see Viewing Additional Display Options on page 102
Note: If you want fluorescent picking on your instrument, the QPix 420
Colony Picking System must be configured with a specific fluorescent imaging
head. For more information, contact technical support at
[email protected].
Note: If you have the fluorescence imaging module, a picking routine just
using white light imaging will take longer because more images are taken.
• Preparing for a Regional Picking Routine on page 85
• Creating and Editing a Regional Picking Routine on page 86
• Running a Regional Picking Routine on page 95
Preparing for a Regional Picking Routine
You need to perform some preliminary steps before successfully conducting a
picking routine. For more information on these steps, see Preparations for
If this is your first picking routine on the QPix 420 System, you must edit the
supplied sanitise profile to suit your needs. For more information on sanitise
profiles, see Creating and Editing Sanitise Profiles on page 61.
Before you begin any new picking routine, Molecular Devices® recommends
you perform a sanitise, UV sanitise, and a manual clean of the interior of the
instrument with ethanol. For more information on these tasks:
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Creating and Editing a Regional Picking Routine
Now that you have created and edited at least one sanitise profile, performed
are ready to create a regional picking routine. This consists of the following
steps:
• Setting Filter Pairs (Fluorescent Light only) on page 89
• Configuring Destination Microplates on page 89
• Setting your Regional Picking Source on page 90
• Defining Destination/Source Options on page 91
1. In the Navigation window, double-click the Picking icon.
2. In the Picking window, click Picking Type and select one of the
following:
 White Light indicates you want to use only white light to illuminate
and identify colonies to pick.
 White Light And Fluorescent (optional feature) indicates you
want white light to illuminate and identify colonies, and fluorescent
light for determining the desired colonies to pick.
3. Click Apply, and then click Start.
To run an existing routine, select Run Existing Routine. This saves
you time by allowing you to choose an existing routine from the Select
Routine list and either editing it, or using it in its exact configuration
(Select Skip Steps for this option).
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Select Skip Steps if you want to keep all existing parameters for
the routine and skip directly to the Settings Summary window.
Delete routines from the Select Routine list by clicking Delete.
If you selected White Light earlier, the Barcodes window appears.
If you selected White Light and Fluorescent The Filter Pair and
Barcodes window appears.

The Filter Pair and Barcodes window allows you to select filter pair and
barcode reading options. For more information on filter pairs, see Setting Filter
Pairs (Fluorescent Light only) on page 89.
data tracking.
Note: If you choose to create validation or manual barcodes they will only be
applied to your source microplates.
1. If you are using the barcode reader, leave the Use Barcode Reader
check box selected (this is the default), and then select a Read Failure
Action option.
search receptacles for barcodes (both source and destination).
section, in case a barcode cannot being read correctly:
receptacles).
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
Skip Receptacle tells the System to cease looking for a barcode
and look for a barcode on the next receptacle (both source and
destination receptacles).
3. Enter your full range of barcodes for this routine in the Validation
Barcode table using the following options.
 From Database means you can import barcodes from a database.
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The Destination Options window opens. For more information, see
Defining Destination/Source Options on page 91.
Setting Filter Pairs (Fluorescent Light only)
If you have selected the fluorescent light option, the Filter Pairs feature is
contained within the Barcodes window. In this case, the window is called
Filter Pairs and Barcodes.
The Filter Pairs section allows you to choose a filter pair.
1. In the Filter Pair Selection section, choose a filter pair from the Filter
Pair list.
2. After you have selected your filter pairs for this routine, click Next. The
Destination Plates window appears.
Configuring Destination Microplates
The Destination Plates window allows you to configure your destination
microplate.
Note: For additional destination options, see Defining Destination/Source
Options on page 91.
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1. In the Destination Plates window, choose a destination microplate
from the Select Destination Microplate list. If you would like to add
a microplate to this list, please contact Molecular Devices to see if we
can add it.
3. Click Make Copy if you want to create a copy of the destination
microplate. If you choose this option, you must also select the other
destination microplate to copy using the Select Copy Microplate list.
Setting your Regional Picking Source
The Source window allows you to configure your source microplate.
Note: Because you are regional picking, you can only select a QTray.
1. In the Regional Source window, configure the picking depth.


Holder displays the default QTray option only, because this is the
only microplate that is designed for regional picking.
Receptacle is greyed out because as you are doing regional
picking, you have no choice but to use the 48-region QTray.
picking pin into the agar in the source tray.
2. Click Next. The Destination/Source Options window appears.

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Defining Destination/Source Options
The Destination/Source Options window is specific to regional picking, and
appears only when you are creating a regional picking routine. Use it to control
your regional picking source and destination options.
1. In the Destination/Source Options window, set your Source
Region Options to limit the number of features (colonies) to be
selected from each region.
 Limit Max. Number Of Features Per Position limits the number
of colonies (Features) per Position (QTray or Petri dish). If you
select this, the Max. Number Of Features Per Position check
box becomes editable.
Note: Selecting this option makes it impossible to change this number
in the Feature Selection section. The number per region will be set
and cannot be changed. For more information on limiting features per
position, see Selecting Colonies on page 98.
If you select this box, you also need to type a number in the
following field:
 Number of Features Per Region allows you to set the limit of
colonies to be selected per region.
 Reserve Wells For Regions allows you to request wells to be left
empty if the number of colonies per region is not reached. For
example, if you had selected 8 colonies per region, but only 6
colonies were eligible for picking, wells 7 and 8 would be left blank.
2. Choose between By Columns or By Rows as the Deposit Order for
the destination microplate.
3. Decide your Deposit Strategy between the following options:
 Fill All Microplates tells the instrument to fill every well of the
 New Microplate For Each Position indicates one QTray or Petri
dish is considered one position. Clicking this means a new
destination microplate will be used when picking begins in a new
position.

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for example when control wells are desired.
The Edit Destination Microplate Template dialog appears. Cleared
wells are displayed in light blue and selected wells are pink.
to re-select it.
6. Click Exit, and then click Next. The Head/Sanitise window appears.
1. In the Head/Sanitise window, choose from the following Picking
Head Options:
 Picking Head allows you to choose various heads.
 Pin Columns Before Inoculation allows you to set the number of
pins available to pick with before inoculation into the destination
microplate. This helps inoculate colonies faster into the destination
microplate (without having to wait until all pins have been used).
 Wash between Partial Inoculation allows you to wash pins
between shorter inoculations.
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Note: If you selected By Rows earlier in the Destination Options
window, you can select 1 to 11 rows, and if you selected By Columns,
you can select 1 to 7 columns.
for both your Destination and Copy receptacles. The Copy field
appears here if you chose Make Copy in the Destination Plates
window. Default values are displayed for each microplate type chosen
earlier.
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The Settings Summary window contains a full summary of the regional
picking routine settings you just configured.
Print a copy of your settings by clicking Print, or click Next.
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Running a Regional Picking Routine
• Creating a White Light Test Image on page 96
• Viewing a Summary of Selected Regional Colonies on page 101
• Loading the Plates on page 103
• Viewing Regional Picking Progress on page 104
• Completing or Running Another Routine on page 105
the microplate holders in the instrument for your picking routine. This is
defined by the selections you made earlier in this routine.
Note: If you do not select Checked? you cannot continue the process.
to click Cancel or press the Stop button on the front of the
instrument.
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2. Click Next. A dialog appears asking you to Please load source.
C
3. After you have loaded the source tray in its correct location, click Next.
The instrument now takes a white light test image of the source tray.
Creating a White Light Test Image
The Test Image window contains the test image and an imaging adjustment
pane. Use these settings to optimize white light settings for picking colonies.
Note: When you are also conducting fluorescent imaging, this window is
labelled WL Test Image in the left menu column to distinguish between the
white light and fluorescent test images.
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view.
 Use Auto Thresholding automatically detects colonies (check box
is selected as a default).
 Use Auto Thresholding adjusts image threshold and colony
detection. Select this check box to manually edit these settings and
move the slider to the position where all the desired colonies are
colored green.
displayed.
to discard detected debris from the images. When excluding debris,
anything excluded will not have a yellow line around it.
measurement.
measurement (in a percentage).
detected after excluding the debris. This dynamically updates.
this processing is completed, the Feature Selection window appears.

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Note: If you selected White Light and Fluorescent at the start of
this routine, clicking Next here starts the fluorescent imaging.
Creating a Fluorescent Test Image (Fluorescent light only)
The Fluorescent Test Image window contains the test image and an imaging
adjustment pane. Use these settings to optimize fluorescent light settings for
picking colonies.
1. Under the Acquisition section, adjust the following:
2. Click Grab Image to save your settings.
3. Click Next.
The System begins “Imaging and Image Processing.” After the image
processing is completed, the Feature Selection window appears.
Selecting Colonies
allowing you to pick colonies of a desired shape, size and proximity.
The primary difference between a standard picking routine and a regional
picking routine is the selection grid overlaid on the imaged colonies with each
region displaying the total number of eligible colonies for picking. This number
is dynamic and will change depending on the selection criteria you set for your
routine.
Note: If your routine consists of both fluorescent and white light imaging, the
Feature Selection window will contain two tabs. Toggle between the two to
select colonies.
The source receptacle with its grid of detected colonies displays in the center
and the barcode for that receptacle is displayed to the right.
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Pickable colonies display in yellow with the total for that region showing as a
number in green. Unpickable colonies (those that are too close to the edge of
the receptacle or do not match your selection criteria) is displayed in red.
Any colony not circled has been excluded from the selection either at the test
image stage, or because it was discarded using the remove debris settings.
If you are performing both fluorescent and white light imaging, the Feature
Selection window contains the following tabs:
• White Light displays everything captured using white light.
• Fluorescent Filter Pair Name (Fluorescent light only) displays
everything captured with the filter pair chosen earlier.
Toggle between the tabs to select colonies.
2. In the Selection section, adjust the following parameters to control
and optimize the size and shape of desired colonies as well as exclude
those colonies that are too close together:
 Compactness sets the level of irregularity for picking colonies. The
irregular shaped colonies will be closer to 0 and regular shaped
colonies will be closer to 1. The System default value is that any
colony equal to or less than 0.65 and will not be picked.
 Axis Ratio measures how oval the colony is. The value is a ratio of
 Min Diameter (mm) sets the minimum diameter of colonies for
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

Min Proximity (mm) sets the distance between colonies to be
Note: Even though the histogram and setting controls are visible on
the White Light tab, they will have no impact on the image. You can
make histogram adjustments only on the Fluorescent tab.
image:
5. (Fluorescent imaging only) Adjust the histogram to obtain the
optimal selection of colonies.
The Histogram displays the level of colony intensity within a selected
image. The peaks show the distribution of the intensity of the colonies.
6. Set intensity measurements with the following settings:


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Mean Intensity is the average fluorescence of the detected colony
(the fluorescence of all the pixels within the colony perimeter
divided by the number of pixels within the colony perimeter).
Median Intensity is the middle fluorescence value of all the pixels
within the detected colony perimeter.
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Geometric Intensity is the geometric intensity of the detect
colony (the fluorescence of all the pixels with the colony perimeter).
 Centre Mean Intensity is the average fluorescence value of the
middle 9 pixels within the detected colony perimeter.
7. Adjust your colony totals with the following settings.

 Limit Colonies limits the total number of pickable colonies. If
Limit Max. Number of Feature Per Region was selected in the
Defining Destination/Source Options section, this option will be
grayed out and the total number of colonies for picking will display.
You cannot change this number.

Viewing a Summary of Selected Regional Colonies
The Feature Counts tab shows the number of colonies detected on a source
along with the number of found colonies, the location of the well (region), as
well as the number of colonies to pick as determined by the selection criteria.
Because you are running a regional pick, the Feature Counts tab
displays information different to a standard picking routine. This tab
displays the following regional picking information:
Well (Regional Picking only) identifies the source tray region based
on its X-Y grid location.
Found states the number of colonies found in that region.
Pickable states number of pickable colonies in that region, based on
your selection criteria.
Picking states number of colonies in that region that will be picked,
based on your selection criteria.
selecting Export.
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The Display Options tab allows you to view additional regional picking
information about the source receptacle image.
Note: Because you are conducting a regional pick, there are additional
picking options under the Display Options tab.
colony selection.
Display Detected Features displays all detected colonies with a
yellow circle when the check box is selected. When not selected,
detected features are not displayed (selected by default).


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Shade Features gives the detected colonies some shading for
clearer visualization. (cleared by default).
Display Numbers Per Region (Regional Picking only) displays
the number of features for each region on the receptacle image. If
you have not placed a limit on the number of features (colonies)
detected per region, all the numbers will display in green. If you
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have created a limit on detectable colonies, the number will display
in green if the criteria are acceptable and red if they are not.
image) where the System is not able to pick. When not selected, the
red hatching is removed from the image (selected by default).
2. Click Next. The Continue or Save New Routine dialog appears.
1. In the Continue or Save New Routine dialog, choose either:
Loading the Plates
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3. Click Next. The picking routine begins, and the Picking Progress
window appears.
Viewing Regional Picking Progress
The Regional Picking Progress window displays a summary of this regional
picking routine, including a timeline to tell you how long to completion.
Note: Remember you can pause the routine by clicking Pause.
During the picking routine, the Regional Picking Progress window displays
the following information:
•
•
•
•
•
•
•
•
•
•
•
•
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StartTime shows the time the picking of the colonies began.
picked from.
Source Region shows the specific region of the source receptacle
being picked from.
Calculate Remaining Time...indicates how far along the routine is.
Pick, when the System is picking.
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Completing or Running Another Routine
When all source micropates have been loaded, the routine is complete.
At this point, the Finished Picking Current Batch dialog appears.
1. In the Finished Picking Current Batch dialog, select one of the
following options:
 Finish Picking ends this picking routine.
 Continue With Image Review allows you to review and edit the
colony selection settings again before running the same routine
with another source tray.
 Continue Without Image Review allows you to run the same
routine again with a difference source tray, but without reviewing
and editing colony selection settings.
2. Click OK.
 If you selected Finish Picking, the Regional Picking Summary
window appears. You can export the information for this routine by
clicking Export.
 If you selected Continue With Image Review, the Test Image
window appears. See Creating a White Light Test Image on page 96
and Creating a Fluorescent Test Image (Fluorescent light only) on
 If you selected Continue Without Image Review, the Please
load source dialog appears. See Running a Regional Picking
Routine on page 95 for a reminder of the necessary steps.
After all picking routines are completed, the Regional Picking
Summary dialog appears, showing the number of source colonies
picked, along with the number of destination microplates used, and any
missing source receptacles.
3. Click Next. The Process Completed window appears.
4. Click Finish to return to the Navigation window.
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The QPix 420 Colony Picking System allows you to create a batch of well
microplates that contain one or more positive control samples, before being
picked into during a standard picking routine. This process is called Control
Plate Creation.
• Preparing for a Control Plate Creation Routine on page 107
• Creating and Editing a Control Plate Creation Routine on page 108
• Running a Control Plate Creation Routine on page 113
Preparing for a Control Plate Creation Routine
You need to conduct some preliminary steps before successfully conducting a
control plate creation routine. For more information on these steps, see
Preparations for Running a Routine on page 59.
If this is your first control plate creation routine on the QPix 420 System, you
must edit the supplied sanitise profile to suit your needs. For more information
on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.
Before you begin any new routine, Molecular Devices® recommends you
perform a manual clean of the instrument interior (using 70% ethanol), and
then conduct a sanitise and UV sanitise. For more information on these tasks:
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Creating and Editing a Control Plate Creation Routine
Now that you have created and edited at least one sanitise profile, conducted
are ready to create a control plate creation routine. This consists of the
following steps:
• Setting Destination Options on page 109
• Setting your Source Receptacle on page 111
• Designating the Control Plate Layout on page 111
1. In the Navigation window, double-click the Control Plate Creation
icon.
2. In the Control Plate Creation window, click Start.
You can also choose the following editing options for routines from
here:
 Run Existing Routine saves you time by allowing you to choose
an existing routine from the Select Routine list and either editing
it or using it in its exact configuration (Select Skip Steps for this
option).
the chosen routine and skip directly to the Settings Summary
window.
The Barcodes window appears.
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data tracking.
1. From the Barcodes window, choose one of the following:
 Use Barcode Reader means the barcode reader will automatically
 Generate Random Barcodes means the instrument generates a
random and unique barcode for every receptacle used (both source
and destination), with prefix Auto. This option prohibits manually
typing barcodes.
The Destination Options window opens.
Setting Destination Options
The Destination Options window allows you to configure your destination
1. In the Destination Options window, choose a destination microplate
from the Select Destination Microplate list. If you do not see a
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Number of Dips tells the instrument how many dips per deposit
 Number of Control Microplates allows you to make duplicates of
the destination microplate (up to 70).
template allows you to clear various wells so that they are not picked
into, for example when control wells are desired. The Edit Destination

Cleared wells are displayed in light blue and selected wells are pink.
to re-select it.
5. Click Exit, and then click Next.
The Head/Sanitise window appears.
profile. For more information on creating sanitise profiles, see Creating and
Editing Sanitise Profiles on page 61.
1. In the Head/Sanitise window, choose a head from the Picking Head
list.
2. Use the Destination field to set the depth (in millimeters) the pin
travels into the bottom of a well of a destination receptacle.
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Note: You cannot edit a sanitise profile from this window. If none of
the sanitise profiles suit your routine, you will need to exit the routine
at this point and create a sanitise profile. For more information, see
Creating and Editing Sanitise Profiles on page 61.
Setting your Source Receptacle
The Source window allows you to configure your source receptacle type as
well as set the picking depth into the agar.
1. In the Source window, choose from the following options related to the
source receptacles for this routine:
Holder selects the source receptacle type.
Receptacle (greyed out) displays source receptacle dimensions.
picking pin into the agar in the receptacle.
2. Click Next. The Control Plate window appears.



Designating the Control Plate Layout
The Control Plate window allows you to designate where the control samples
are placed on the destination receptacle.
1. From the Control Plate window, click the location of the desired wells
in the destination receptacle map (on the right).
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For a multiple well selection, you can also left-click drag the cursor over
multiple wells in the destination map.
2. When you are satisfied with the layout of the control samples in the
destination receptacle map, click Next. The Settings Summary
window appears.
settings you just configured.
Print a copy of the settings by clicking Print, or click Next to continue.
Note: Once you click Next here, you can no longer click the Back
button to return to a previous window.
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Running a Control Plate Creation Routine
• Loading Source Receptacles on page 114
• Creating a Test Image on page 114
• Viewing a Summary of Selected Colonies on page 118
• Viewing the Picking Progress on page 120
• Viewing the Summary of Your Routine on page 120
routine. This is defined by the selections you made earlier in this
routine.
2. Click Next. The Please load source window appears.
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Loading Source Receptacles
The Please Load Source window is a visual aid for installing the source
microplates correctly in the instrument.
1. Load the source receptacles in their correct location.
2. Click Next. The instrument now takes a white light test image of the
source receptacle.
Creating a Test Image
The Test Image window contains the test image and an image adjustment
pane. Use these settings to optimize your selection settings.
Note: All detected objects are viewed as features, so to ensure you are
detecting colonies not debris, use Remove Debris in this part of the routine.
view.
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Gain allows you to increase the image signal without increasing the
Use Auto Thresholding automatically detects colonies (check box is
selected as a default). Deselect this check box to manually edit these
settings and move the slider to the position where all the desired
colonies are colored green.
displayed.

to discard detected debris from the images. When excluding debris, any
object that is excluded will not have the yellow line circling the detected
object.
measurement.
measurement (in a ratio of roundness).
detected after excluding the debris. This dynamically updates with
your changes.
the imaging, the Feature Selection window appears.

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Selecting Colonies
allowing you to pick colonies of a desired shape, size and proximity, and
fluorescent intensity.
An image of the source receptacle with its detected colonies is displayed in the
center and the barcode for that receptacle is displayed to the right.
Pickable colonies are displayed in yellow, while unpickable colonies (those that
are too close to the edge of the receptacle or do not match your selection
criteria) are displayed in red.
Any colonies with no circle were excluded in the test image stage because they
fell within the remove debris settings.
2. In the Selection section, adjust the following parameters to control
and optimize the size and shape of desired colonies as well as exclude
those colonies that are too close together:
 Compactness sets the level of irregularity for picking colonies. The
irregular shaped colonies will be closer to 0 and colonies that are
more of a perfect circle are closer to 1. The System default value is
that any colony equal to or less than 0.65 and will not be picked.
 Axis Ratio measures how oval the colony is. The value is a ratio of
 Min Diameter (mm) sets the minimum diameter of colonies for
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 Min Proximity (mm) sets the distance between colonies to be
image:

5. Adjust your colony totals with the following settings:
 Limit Colonies (not applicable for Control Plate Creation, and as
such this remains greyed out).

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The Feature Counts tab shows the number of found features on a source
along with the number of found colonies, as well as the number of colonies to
pick as determined by the selection criteria.
selecting Export.
source receptacle image.
colony selection.
Display Detected Features displays all detected features with a
yellow circle when the check box is selected (default). When not
selected, detected features are not displayed.
 Shade Features gives the detected colonies some shading for
clearer visualization (unselected by default).
image) where the System decides it is not safe to pick (default). When
not selected, the shading is removed from the image.
2. Click Next. The Continue Or Save New Routine dialog appears.
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following:
Loading the Plate Holders
3. Click Next. The picking routine begins, and the Picking Progress
window appears.
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Viewing the Picking Progress
The Picking Progress window displays a summary of this routine, including a
timeline to tell you how long to completion.
•
•
•
•
•
•
•
•
•
•
•
•
When
picked from.
Estimated Time Remaining indicates remaining time.
Pick, when the instrument is picking.
Light Table Off allows you to switch off the light table light in the
instrument.
your routine is finished, the Picking Summary window appears.
Viewing the Summary of Your Routine
After your routine is complete, the Picking Summary dialog appears,
showing the number of source colonies picked, along with the number of
destination microplates used, and any missing source receptacles.
1. Choose from one of the following options:
 Click Export to save this information into a .csv file.
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
Click Details to open the Picking Details dialog and view full
information of all activities related to the source and destination
receptacles. Click Export from here to save the information to a
.csv file. Click Close to return to the Picking Summary window.
2. Click Next, and then click Finish to return to the Navigation window.
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The QPix 420 Colony Picking Software gives you the following three options to
replicate your samples from one microplate to another:
• Library Replication replicates between microplates with the same
number of wells.
• Library Compression replicates from 96-well microplates to 384 wellmicroplates (compresses the samples).
• Library Expansion replicates from 384-well microplates to 96 wellmicroplates (expands the samples).
Note: The process for conducting all three replication routines are very
similar, so they will all be covered in this chapter. Differences and exceptions
will be clearly identified and explained.
• Preparing for a Replicating Routine on page 123
• Creating and Editing a Replicating Routine on page 124
• Running a Replicating Routine on page 128
Preparing for a Replicating Routine
You need to conduct some preliminary steps before being able to successfully
replicate your colonies. If this is the first time you have ever conducted a
replicate on the QPix 420 Colony Picking System, you must edit the supplied
sanitise profile to suit your needs.
• For more information on completing this task, see Creating and Editing
Remove any loose items from the interior of the instrument, and wipe them
down too. Finally, remember to top up your wash baths with relevant cleaning
fluids.
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Creating and Editing a Replicating Routine
Now that you have conducted both sanitise routines and given the instrument
interior a manual clean, you are ready to create a replicating routine. This
consists of the following steps:
• Setting Microplate and Sanitise Options on page 127
• Setting Head Options on page 128
• Viewing the Replication Progress on page 131
• Viewing the Replicating Process Summary on page 131
conduct the following steps to create and edit a replicating routine:
1. In the Navigation window, double-click the Library Replication icon,
then click Start.
here:
option).
window.
The Barcodes window allows you to select your barcode reading options.
data tracking.
Note: If you choose to use validation or create manual barcodes they will
only be applied to your source microplates, and the instrument will look only
for the number of microplates listed to plate.
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Action option.
receptacles).
 Skip Receptacle tells the System to cease looking for a barcode
3. If validating barcodes, enter your full range of barcodes for this routine
in the Validation Barcode table using the following options.
 From Database allows you to import barcodes from the database.
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The Microplates/Sanitise window opens.
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Setting Microplate and Sanitise Options
The Microplates/Sanitise window allows you to define your source and
destination microplate types, choose multi-dipping and stirring, create
additional copies (Library Replication only), and replicate from multiple
source microplates. You also choose your sanitise profile from this window.
1. In the Microplates window, select source and destination receptacles
from the Source Microplate and Destination Microplate lists.
 With Library Replication, the two lists in the Microplate Options
section allow you to select only microplates with the same number
of wells (the other list changes its microplate selection options
based on your most recent selection).
 With Library Compression, the two lists in the Microplate
Options section allow you to select only relevant microplates
related to compression (96-well to 384-well). The Source
Microplate list contains only a selection of 96-well microplate
options, and the Destination Microplate list contains only 384well microplate options.
 With Library Expansion, the two lists in the Microplate Options
section allow you to select only relevant microplates related to
expansion (384-well to 96-well). The Source Microplate list
contains a selection of 384-well microplate options, and the
Destination Microplate list contains 96-well microplate options.
2. From the Microplate Options section, choose from the following
additional options for your source, destination or both microplates:
microplate well multiple times.
 Number of Dips tells the instrument how many dips per microplate
well you want it to make.
 Stir Source stirs the pins in the source microplate wells. If you
choose this option, you cannot multi-dip.
3. With Library Replication, if you want to make additional copies during
this routine, set a number (up to two) in the Additional Copies field.
The Sanitise Between Copies check box becomes ungreyed if you
select this option, allowing you to set additional wash cycles.
4. Use the Number of Source Microplates list if you are using multiple
source receptacles (maximum 100). The Number of Source Per Bed
field automatically updates (maximum 10) and notifies you how many
source receptacles you can place on QPix 420 interior bed based on
how many source receptacles you are using for the routine.
5. Choose a sanitise profile from the Sanitise Profile list.
For more information on creating or editing sanitise profiles, see
6. Click Next. The Head window opens.
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Setting Head Options
The Head window allows you to select the head type, and set inoculation
dipping heights for both Source and Destination microplates.
1. In the Head window, select a head type from the Select Head list.
2. Set your inoculation heights in the Source and Destination fields.
These set the depth above the bottom of a well that the pin travels to.
3. Click Next. The Holder Layout window appears.
Running a Replicating Routine
• Arranging the Layout for the Routine on page 128
• Viewing the Replication Progress on page 131
• Viewing the Replicating Process Summary on page 131
Arranging the Layout for the Routine
routine. This is defined by the selections you made earlier.
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Click Next. The Load Plates window appears with instructions on
where to place the source and destination microplates on the plate
holders.
2. Follow the layout instructions in the Load Plates window (including
removing all microplate lids), and after you are certain you have loaded
everything correctly, click Checked?
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The Settings Summary window contains a summary of the routine settings
you just configured. You can print a copy of these by clicking Print.
From the Settings Summary window, click Next. The Continue or Save
New Routine dialog appears.
following:
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To save this routine, select Save Routine, type a Name and
Description in the relevant fields, and then click Save.
The replication routine begins. The instrument reads the barcodes, and
the Library Replication Progress window appears.
Viewing the Replication Progress
The Library Replication Progress window displays the following details:
• Start Time displays the time the replicating of samples began.
• Source Plate No shows the source microplate being replicated.
• Source Barcode shows the barcode of the source receptacle being
replicated.
• Source Offset displays the source well into which the pins will be
lowered. This changes if using a 384-well microplate.
• Depositing into displays the well or microplate the sample will be
deposited into.
• Destination Plate No displays the current destination microplate
number that is being replicated into.
• Destination Barcode displays the current destination microplate
barcode that is being replicated into.
• Destination Offset shows the destination well into which the pins will
be lowered. This will change if using a 384-well microplate.
• Calculate Remaining Time...indicates how far along the routine is.
Note: The QPix 420 System will ask for more source microplates to replicate.
Viewing the Replicating Process Summary
After the replicating routine has been completed, the Replicating Process
dialog appears, showing the number of source wells replicated, along with the
number of destination microplates used, and any missing source microplates.
You have the following options from this window:
• Click Export to save this information into a .csv file.
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•
Click Details to open the Replicating Details dialog and view full
receptacles. Click Export from here to save the information to a .csv
file. Click Close to return to the Replicating Process window.
•
Click Next, and then click Finish to return to the Navigation window.
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Conducting a Rearraying Routine
10
Performing Rearraying Procedures
The QPix 420 Colony Picking Software allows you to re-deposit (rearray)
colonies between one or more source and destination microplates. You would
do this if you wanted to organize (cherry-pick) your picked source colonies into
destination subsets of a more specific and orderly layout.
The following sections are described here:
• Preparing for a Rearraying Routine on page 133
• Creating and Editing a Rearraying Routine on page 133
• Running a Rearraying Routine on page 138
Preparing for a Rearraying Routine
You need to perform some preliminary steps before being able to successfully
rearray your picked colonies. If this is the first time you have ever performed a
rearray on the QPix 420 Colony Picking System, you must edit the supplied
sanitise profile to suit your needs.
• For more information on completing this task, see Creating and Editing
Before you begin any new replicating routine, Molecular Devices®
recommends you perform a sanitise, UV sanitise, and a manual clean of the
interior of the instrument with ethanol. For more information on these tasks:
Remove any loose items from the interior of the instrument, and wipe them
down too. Finally, remember to top up your wash baths with relevant cleaning
fluids.
Creating and Editing a Rearraying Routine
Now that you have performed both sanitise routines and given the instrument
interior a manual clean, you are ready to create a rearraying routine. This
consists of the following steps:
• Identifying your Source Receptacle on page 135
• Defining your Destination Receptacle on page 137
Perform the following steps to create and edit a rearraying routine:
1. In the Navigation window, double-click the Rearraying Icon, and then
click Start.
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here:
option).
window.
 Delete routines from the Select Routine list by clicking Delete.
The Barcodes window allows you to select your barcode reading options.
data tracking.
Action option.
receptacles).
 Skip Receptacle tells the System to cease looking for a barcode
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The Source window opens.
Identifying your Source Receptacle
The Source window allows you choose source microplate details and head
behaviour, and input receptacle identifier information.
1. From the Source window, select a receptacle from the Source
Microplate list, and select source microplate data in the following
ways:
Import inputs all source microplate data from a .txt or .csv file to the
table. You can also use .frd (Fusion) and .imp (legacy QSoft) files.
From Database imports source data from the software database.
Clicking this button opens the Barcode Search window with the
following tabs:
 By Tag conducts a tag search. Tags improve the ability to identify
and search for any routine, receptacle, or location (colony). For
more information on tags, see Working with Tags on page 162.
 By Process searches for barcodes from previous routines.
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Navigate to a completed routine in the table on the left, select a source
barcode from the Barcode table on the right, and then click Add
Barcode. That barcode now appears in the Selected Barcodes table.
2. Click Import or Remove Barcode to continue.
 Insert opens an editable image of the receptacle where you can
define the wells you want to pick from for your rearraying routine.
 Export allows you to export source microplate data to a .frd
(Fusion) or .imp (QSoft) file.
3. After you have added at least one microplate identifier to the Source
window table, you can Edit, Remove, or Remove All the entries.
4. Select Stir Source if you want the head to stir the source before
depositing it in a receptacle well.
5. Type a number in the Microplates to Process Before Depositing
field to define the quantity of microplates to process before depositing.
6. Click Next.
The Destination window appears.
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Defining your Destination Receptacle
The Destination window allows you to define your destination receptacle.
1. In the Destination Microplate Options section, choose a destination
microplate from the Select Microplate list. If you do not see a
2. Choose from the following additional options for your destination
microplates:
source receptacle multiple times per dip.
3. In the Deposit Order section, choose between By Columns or By
Rows as the Deposit Order for the destination receptacle.
4. Click Edit to edit the Destination Microplate Template. This
for example when control wells are desired. The Edit Destination
Cleared wells are displayed in light blue and selected wells are
displayed in pink.
to re-select it.
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6. Click Next. The Head and Sanitise window appears.
The Head and Sanitise window allows you to pick a head and select a
sanitise option. For more information on sanitise profiles, see Creating and
1. In the Head and Sanitise window, choose a head from the Select
Head list.
for both your Source and Destination microplates. Default values are
displayed for each microplate type chosen earlier.
Running a Rearraying Routine
• Confirming the Layout for the Routine on page 139
• Viewing the Rearraying Progress on page 141
• Viewing the Rearraying Process Summary on page 141
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Confirming the Layout for the Routine
The Holder Layout window appears with instructions on setting the bed levels
and loading the correct head and wash bath.
Note: Because rearraying requires five plate holders, you must ensure the
imaging table has been removed before continuing.
1. Follow the layout instructions in the Holder Layout window (including
removing the imaging table).
2. After you are certain you have loaded everything correctly, click
Checked?
3. Click Next. The Load Plates window appears with instructions on
where you need to place the source and destination microplates on the
plate holders.
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to press the Stop button on the front of the instrument.
The Settings Summary window appears with a full summary of all the
settings you have made for this routine.
1. Print a copy of your settings by clicking Print, or click Next to
continue.
WARNING! After clicking Next here, you can no longer click Back.
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Viewing the Rearraying Progress
•
•
•
•
•
•
•
•
•
•
•
•
Source Plate No shows number of the source receptacle.
Source Barcode shows the barcode of source receptacle being picked.
Destination Plate No shows the number of the destination receptacle.
Total Wells Rearrayed is the number of wells rearrayed so far.
Total Wells to Rearray is the total number of wells to be rearrayed.
Estimated Time Remaining indicates how far along the routine is.
Deposit, when the System is depositing.
•
Viewing the Rearraying Process Summary
After the rearraying routine has been completed, the Rearraying Process
dialog appears, showing the number of source wells rearrayed, along with the
number of destination microplates used, and any missing source microplates.
1. In the Rearraying window, click Next. The Process Completed
window appears.
2. In the Process Completed window, click Finish to return to the
Navigation window.
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Gridding Processes
11
Gridding allows you to deposit liquid samples from one or more source
microplates to one or more destination surfaces (either agar filled QTrays or
filters).
• Preparing for a Gridding Routine on page 143
• Creating and Editing a Gridding Routine on page 143
• Running a Gridding Routine on page 154
Preparing for a Gridding Routine
You need to conduct some preliminary steps before successfully conducting a
gridding routine. For more information on these steps, see Preparations for
If this is your first gridding routine on the QPix 420 Colony Picking System, you
must edit the supplied sanitise profile to suit your needs. For more information
on sanitise profiles, see Creating and Editing Sanitise Profiles on page 61.
Creating and Editing a Gridding Routine
Now that you have created and edited at least one sanitise profile, conducted
are ready to create a gridding routine. This consists of the following steps:
• Setting Source and Destination Receptacles on page 146
• Creating a Filter Design Layout on page 147
• Selecting the Destination Tray on page 152
• Selecting Stamping and Inking Options on page 153
• Viewing the Gridding Progress on page 157
Conduct the following steps to create and edit a gridding routine:
1. In the Navigation window, double-click the Gridding icon.
2. In the Gridding window, click Start.
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Gridding Processes
here:
option).
window.
data tracking.
1. If using the barcode reader, leave the Use Barcode Reader check box
selected (default), and then select a Read Failure Action option.
section, in case a barcode cannot be read correctly:
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

Manual prompt launches a dialog where you can manually type a
receptacles).
Skip Receptacle tells the instrument to cease looking for a
barcode and look for a barcode on the next receptacle (both source
and destination receptacles).
3. If validating barcodes, enter your full range of barcodes for this routine
in the Validation Barcode table using the following options.
 From Database allows you to import barcodes from the database.
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Gridding Processes
The Head window opens.
The Head window allows you to select a relevant gridding head and choose a
sanitise profile. For more information on sanitise profiles, see Creating and
1. In the Head window, choose a head from the Gridding Head list.
Note: You cannot edit a sanitise profile from this window. If none of
the sanitise profiles suit your routine, you will need to exit the routine
at this point and create a sanitise profile. For more information, see
3. Click Next. The Microplates and Filters window appears.
Setting Source and Destination Receptacles
The Microplates and Filters window allows you to set up the source
receptacles and destination surface, as well as control the number of times the
head dips into the source receptacle or stirs the source solution.
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1. From the Select Microplate list, select the appropriate microplate to
suit the stacker configuration of your instrument.
Choose from the following additional options:
receptacle multiple times.
 Number of Dips tells the instrument how many dips you want it to
make.
 Stir Source stirs the pins in the source receptacle wells. If you
choose this option, you cannot multi-dip.
 Inoculation Heights (mm) allows you to set the depth the pin
travels to above the bottom of the receptacle well. By default, the
pin drops as low as possible into the well.
2. From the Select Receptacle list, choose either QTray or Filter.
3. Click Next. The Filter Design window appears.
Creating a Filter Design Layout
The Filter Design window allows you to arrange how spot and field patterns
can be stamped (gridded) onto destination receptacles - QTray or filter.
You can choose existing spot patterns from the Reuse list, but only if some
spot patterns have been previously created and saved. If there are no existing
spot patterns (if the Reuse list, and Load and Delete buttons are greyed
out), you will need to create a new spot pattern.
Spot Patterns refer to the pattern and number of times that one pin will
stamp onto the destination QTray.
Field Patterns refer to the way that the QTray is divided up into sections. The
fields match the dimensions of a 96-pin head. One field equals one head.
Note: There is no visual correlation between Spot Pattern and Field Pattern,
despite both patterns using the same colouring and numbering formats.
There is a great amount of flexibility with the Filter Design options.
The default setting is to be able to fill your QTray with a maximum of 14,400
different samples (6 fields times 25 spots per pin times 96 pins) originating
from 150 different 96-well source microplates (see image below).
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Gridding Processes
o
At the other end of the range, assuming you were using 1 filled 96-well source
microplate, the minimum number of samples being stamped onto your QTray
would be 96 different samples (1 field times 1 spot per pin times 96 pins) (see
image below).
You can create any number of different filter designs (field and spot patterns)
within this range.
Note: The Filter Design window defaults to the maximum possible settings
for the Field Pattern (6 fields) and Spot Pattern (25 spots per pin). You can
change all of these settings to whatever you want.
1. From the Reuse section of the Filter Design window, If there is at
least one existing spot pattern in the Reuse list, you can make a
selection from the Reuse list, and click Load. The Load Gridding
Pattern? dialog appears, and notifies you that loading this pattern will
overwrite the current spot pattern. Click Yes to confirm.
 Click Save to save a customized spot pattern separately from the
whole routine (field pattern is not saved). The Save New Gridding
Pattern? dialog appears. Type a name in the Name field and click
OK. The new name is instantly available from the Reuse list.
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Click Delete to remove a spot pattern from the Reuse list. The
Delete Gridding Pattern? dialog appears. Click Yes to delete.
If there are no spot patterns in the Reuse list, or if none of the existing
spot patterns match your needs, you will need to create one.
2. From the Structure section, set the number of Rows and Columns to
be stamped for each pin, and create the Spot Pattern per pin.
Your spot pattern must have a logical numerical sequence to it (for
example: 1,2,3,4 or 1,2,2,4). If you create an illogical sequence to the
Rows or Columns fields (for example: 1,3,4,3 or 1,4,1,2), an error
message at the bottom of the window displays “Can’t Calculate” in
red text, a No Sequence button displays in red, and the Spot Pattern
is cleared (blank yellow circles) until you select your Fill options to set
your spot pattern automatically.
The Next button also becomes greyed out, making it impossible to
progress from this page.

3. From the Fill section, select a Replicate (copy) quantity (between 1
and 4), and click one of the eight direction buttons to confirm where
you want the number 1 pin to start, along with the gridding direction
you want the spot pattern to follow.
The Spot Pattern displays the layout of the new spot pattern in
coloured circles (n rows, n columns, n replicates), and the Sequence
Complete button changes colour from red to green. Spots with the
same colour and number indicate that the same sample will be spotted
in those positions within the spot pattern, and spots with different
numbers and colours indicate that different samples will be spotted in
those positions within the spot pattern.
Click Clear Spots, and then click OK in the Clear Pattern? dialog to
clear the current spot pattern while keeping the same pattern
structure.
Note: The Structure and Spot Pattern sections of the Filter Design
window are highlighted and other sections removed in the following two
images, to highlight the effects of changing numbers in the Rows and
Columns fields.
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Gridding Processes
The higher the number in the Rows and Columns fields, the more
spots per pin for the spot pattern, and the smaller the Row Pitch and
Column Pitch (maximum space between each spot in the spot
pattern) will be. These numbers change dynamically depending on your
Rows and Columns settings.
You can reduce the Row Pitch and Column Pitch but you cannot
exceed the displayed maximum measurements (ums) in these fields.
4. To create a spot pattern automatically, click any of the eight direction
buttons, and then click OK in the Fill Pattern? dialog to change the
current gridding direction.
5. You can make manual changes to the Spot Pattern (only in Layout
View) by highlighting a circle and either typing a new number for that
circle, or clicking the Clear Spots button or pressing the Delete key to
clear the colour and number.
However, if your subsequent sequence or pattern is incorrect, the
Sequence button displays Sequence Incomplete in red text, an error
message displays “Can’t Calculate” in red text at the bottom of the
window, and the Spot Pattern Status dialog appears, describing the
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error and instructions on the necessary fix. Also, the Next button
becomes greyed out, making it impossible to continue from this page.
6. From the View section, click Actual View to see a realistic
representation of the layout and spot pattern of the pins.
Type any number up to 1500 into the Estimated Spot Size field to
change the representation of the spot size (default is 200 um) in the
Actual View of the Spot Pattern section. (The Field Pattern and Fill
sections have been excluded from this image to simplify the view).
7. From the Field Pattern section, select any field and type any number
between 1 and 6 to create the desired layout of the destination surface.
Note: You can grid your samples on up to 2 QTrays or 6 filters.
However, the software creates one field pattern per routine (printed
onto either destination receptacle), so whatever pattern you choose
will be replicated onto the chosen number of receptacles (QTrays or
filters) used for that routine.
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Gridding Processes
Each field represents one head stamp. By default, 6 different fields
display in the Field Pattern section, meaning that each field will
contain different samples.
The large green number in the lower section of the window (in this
example, 12) indicates the number of microplates required to fulfill this
gridding pattern (number of different spots in the Spot Pattern times
the number of different field patterns in the Field Pattern).
8. To change the Field Pattern layout, click a field and type any
sequentially logical number between 1 and 6.
To create a blank field, click the field, and then hit the Delete key.
If the layout contains two identical fields (same colour and number),
this means the fields will be replicates (copies).
If you create a numerically illogical field pattern (for example:
1,1,2,5,3,5), the Sequence button changes from green text
(Sequence Complete) to red text (Sequence Incomplete).
For information about the error and how to fix it, click the Sequence
Incomplete button, and view the Field Pattern Status dialog.
Click OK and type in a sequentially logical number (in this example, 4).
9. Click Next. The Filter Layout window appears.
Selecting the Destination Tray
The Filter Layout window allows you to choose only the QTray as your
destination receptacle. The other options are greyed out.
Click Next. The Substrate window appears.
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Selecting Stamping and Inking Options
The Substrate window allows you to select stamping and inking options.
1. From the Substrate window, set a number (between 1 and 5) in the
Stamps Per Spot field. This allows you to increase the amount of
samples spotted in one location. If you set a number more than one
here, the Re-Ink After #of Stamps check box becomes ungreyed.
2. Check the Re-Ink After # of Stamps box if you would like the head to
return to the source plate to re-ink the pins before stamping the
samples again, and choose the quantity of re-inks (between 1 and 10).
3. If you have chosen to re-ink the pins after stamping, select one of the
following radio buttons to define what re-inking method you would like:
 Cyclic means stamp all sample spots once before re-inking.
 Immediate means re-ink right after the first spot is stamped.
4. Choose Stamp Time (ms) and Dwell Time (ms) settings for how
long you want the pin pressed against the destination surface (Stamp
Time), and how long you want the pins submerged in the source well
(Dwell Time).
5. Choose a number (between 1 and 15) in the Overtravel Adjustment
(mm) field for the pins to travel an extra distance and ensure they all
touch a potentially uneven receptacle surface firmly enough for a good
transfer of all samples.
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Gridding Processes
Running a Gridding Routine
• Viewing the Gridding Progress on page 157
Arranging the Layout for the Routine
routine. This is defined by the selections you made earlier.
o
2. Click Next. The Load Plates window appears with instructions on
where to place the source and destination microplates.
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The Settings Summary window contains a full summary of your routine.
1. Print a copy of the settings by clicking Print, or click Next to continue.
The Continue Or Save New Routine dialog appears.
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Gridding Processes
following:
The Please Load Destination window appears.
After you have loaded your source receptacles in their correct location inside
the instrument, click Next. The Gridding Progress window appears and the
gridding routine begins.
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Viewing the Gridding Progress
The Gridding Progress window displays a summary of this routine, including
a timeline to tell you how long to completion.
•
•
Start Time shows the time the gridding began.
Source Plate No shows the current source microplate that is being
gridded from.
• Source Barcode shows the barcode of the source microplate being
picked from.
• Destination Receptacle No is current destination surface being
gridded onto.
• Destination Barcode is the barcode of the destination surface being
gridded onto.
• Field is the current destination field being gridded.
• Spot is the current destination spot being gridded.
• Field Replicate is the current destination field replicate being gridded.
• Spot Replicate is the current destination spot replicate being gridded.
• Stamp is the current stamp being gridded.
When the routine is completely finished, the Gridding Summary window
appears.
Viewing the Summary of Your Routine
After your routine is complete, the Gridding Summary dialog appears,
showing the number of spots stamped, along with the number of source
microplates reaped, and any missing source receptacles.
1. Choose from one of the following options:
 Click Export to save this information into a .csv file.
 Click Details to open the Gridding Details dialog and view full
barcodes and destination regions and locations. Click Export from
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here to save the information to a .csv file. Click Close to return to
the Picking Summary window.
2. Click Next, and then click Finish to return to the Navigation window.
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12
The Data Viewer window allows you to view data details from the full set of
previous routines run on the QPix 420 Colony Picking System.
The following procedures are described here:
• Conducting a Data Search on page 159
• Working with Tags on page 162
• Adding Annotations on page 164
• Exporting Processes or Routines on page 165
• Adding or Deleting Properties for Microplates on page 165
• Viewing a Map of the Locations on page 167
• Working with Sample Trails on page 168
Conducting a Data Search
1. In the Navigation window, double-click the Data Viewer icon. The
Data Viewer window opens.
2. Using the navigation menu on the left, choose the particular routine
you want by either one of the processes (Picking, Regional Picking,
Rearraying, or Replicating), or by selecting one of the following
specific search parameters:
 By Tag. For more information on searching by tags, see Searching
by Tag on page 160. For more information on creating and editing
tags, see Working with Tags on page 162.
 By Barcode. For more information on searching by barcodes, see
Searching by Barcode on page 160.
 By Date. For more information on searching by date, see Searching
by Date on page 161.
 By User. For more information on searching by user, see Searching
by User on page 161.
 By Location. For more information on searching by location, see
Searching by Location on page 161.
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3. Single-click any routine in the table to display related barcoded
receptacle and annotation details at the bottom of the window.
Max
If necessary, click More in the Barcoded Receptacles window, to
view additional receptacles in the Destination Receptacles window.
Click Close to return to the Processes window.
Searching by Tag
The Search by Tag window allows you to search receptacles based on any
given tags. Select the required tag from the Available Tags field, and then
click Add. Search results for the tag display at the bottom of the window.
Double-clicking any of these results displays more details related to the item.
For more information about tags, see Working with Tags on page 162.
Searching by Barcode
The Search by Barcode window allows you to search receptacles by any
barcode. If found, the search results display below. Double-clicking any of
these results displays more details related to the item.
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Searching by Date
The Search by Date window allows you to search for a routine based on the
date it was run. All data produced on that date displays in the table below.
Searching by User
The Search by User window allows you to search by user from the User list.
Searching by Location
The Search by Location window allows you to search by location of wells.
Select the required Well or Barcode to search for the desired data set.
Viewing and Printing Settings Details
1. To view and print every setting configured for your chosen routine, click
a process from the Processes menu on the left, double-click a specific
routine in the Processes table on the right, and then click Settings
from the subsequent window.
The View Settings window appears. Items will be different in this
window, based on whether you are looking at details of a picking,
rearraying, or replicating routine.
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2. Click Print to print these settings, or Exit to return to the previous
window.
Working with Tags
A tag is a user-created identifier for a routine, receptacle, or location. Use tags
to easily identify data of interest. You can create, add, or remove tags from the
menu in the Data Viewer window. You can create a tag at any time, but can
only add or remove a tag after selecting a routine from the Processes table.
For information on searching by tags, see Searching by Tag on page 160.
Creating a Tag
Tags can be created from anywhere within the Data Viewer window.
1. From the Data Viewer window, click Create Tag. The Create Tag
dialog appears.
2. Type the tag name in the Tag field, and if relevant, type a description in
the Description field.
3. Click Create Tag, to return to the Data Viewer window. This new tag
will now be available to add to relevant data.
Adding Tags to a Receptacle, Location, or Routine
Once you have created at least one tag, you can add it to any routine,
receptacle, or location (well or position in a QTray or Petri dish).
1. From the Data Viewer window, navigate to the desired routine,
receptacle, or location, and then click Add Tag in the navigation menu
on the left. The Select Tags to Add dialog appears. Depending what
level of detail you have navigated to, this dialog will display radio
buttons for either Process, Process and Receptacle, or Process,
Receptacle, and Location.
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2. Select the relevant radio button based on the level you want to tag, and
select a tag name from the table.
3. Click Add Tags. The Data Viewer window appears, with the tag name
(in this example: qtray) displayed in the right side menu.
Removing a Tag
You can remove a tag from any process, receptacle, or location.
receptacle, or location. If the item has a tag associated with it, the tag
name will appear in the right side menu.
2. Click Remove Tag in the navigation menu on the left. The Select Tags to
Remove dialog appears.
3. Select the tag you wish to remove, and then click Remove. The tag is
removed and the Data Viewer window appears.
5026152 A
163
Adding Annotations
You can add annotations (notes) to any routine, receptacle, or location once
you have selected a specific routine.
receptacle, or location, and then click and then click Add Annotation
in the left navigation menu. The Add Annotation dialog appears.
2. Type the relevant annotation text, and then click the radio button for
the level where you want the information added (Process, Receptacle
or Location).
3. Click Add. The dialog closes and the annotation now displays in the
Annotations table at the bottom of the window.
164
5026152 A
Exporting Processes or Routines
You can export a full list of processes or routines to either a .csv file
(Processes) or HTML file (Routine settings).
1. From the Data Viewer window, navigate to the desired process or
routine, and then click one of the following:
Export Process saves all data related to the selected process into an
Excel .csv spreadsheet.
Export Routine saves all data related to the routine in an HTML file.
2. Navigate to where you want to save the file, and then click Save.
Adding or Deleting Properties for Microplates
You can add or delete additional property information related to any microplate
well in the Location Properties table.
Adding Properties
Note: This task is performed only at the microplate well level.
1. From the Data Viewer window, navigate to the relevant microplate
level, and then click Add Property. The Add Property dialog appears.
2. Type a relevant name for the additional property you want to add to
this microplate data in the Property Name field, and type a relevant
value in the Property Value field.
3. Choose one of the following categories from the Property Type list:
 String holds text (for example: Positive Sample)
 Int holds integer values (for example: 5)
 Double holds decimal numbers (for example: 6.75)
 Bool holds a boolean value (for example: True)
4. Click Add. The Add Properties dialog disappears, and the new
property information displays in the Location Properties table to the
right of the microplate image.
5026152 A
165
Deleting a Property
level, and then select the specific property you wish to delete from the
Location Properties table.
Note: You can only delete properties that have been added to the existing
default properties. Default properties cannot be deleted.
2. Click Delete Property. The Delete Property dialog appears.
3. Click Delete Property, and when you return to the previous window,
that property will no longer display in the Location Properties table.
166
5026152 A
Viewing a Map of the Locations
You can view the connections of colonies that have been mapped from one
receptacle to another by clicking Show Locations Map.
well level, and then select a well that you would like to map its location.
2. From the left navigation menu, click Show Locations Map. The
Location Map dialog appears, showing the path that the well of
interest has followed.
3. Click Close to return to the previous window.
5026152 A
167
Working with Sample Trails
You can view details on how one or more wells were used in a particular
routine by using Sample Trails. Until you have added at least one sample
trail, the Display Sample Trail and Clear Sample Trail options remain
greyed out.
Adding and Removing Sample Trails
1. From the Data Viewer window, navigate to the relevant microplate.
2. Click Add/Remove. The Edit Sample Trail dialog appears.
3. Select the desired wells. To de-select a well, click it again.
4. Click OK to return to the previous window. The selected wells are now
displayed in the Sample Trail tail, and Display Sample Trail and
Clear Sample Trail are now clickable.
168
5026152 A
5. To remove the sample trail, click Add/Remove, and deselect the
relevant wells.
Viewing and Clearing Sample Trails
1. From the Data Viewer window, click Display Sample Trail. The Sample
Trail Locations dialog appears, with sample property and location
details of all the sample wells selected in the Edit Sample Trail dialog.
2. Click Close to return to the previous window.
To save the information as a .csv file, click Save and navigate to the
relevant save location.
3. To clear the total sample trail click Clear Sample Trail. All information
is immediately deleted and removed from the Sample Trail table.
5026152 A
169
170
5026152 A
Replacement Parts and Optional Extras
A
Please refer to the Molecular Devices® website for the latest replacement
parts and optional extras at:
www.moleculardevices.com/genetix
Table A-1: QPix 420 Colony Picking System Replacement Parts
Code
Description
X4006J
Phage picker+ picking head, 96 pin, tip diameter 1.6 mm, deep well
X4006K Yeast picker+ picking head, 96 pin, tip diameter 1.6 mm, deep well
X4300
Picking Head 96-pin
X4310A Re-arraying and replicating head, standard transfer, 96 pin for 96- &
384-well microplates, tip diameter 0.55 mm, pin length 49.5 mm
X4310B Re-arraying and replicating head, hi-capacity transfer, 96 pin for 96& 384-well microplates, tip diameter 1.6 mm, pin length 49.5 mm
X4370
Picking pin for E.coli/phagemid, tip diameter 0.55 mm
X4371
Picking pin for phage plaque, tip diameter 1 mm
X4372
Picking pin for yeast, tip diameter 1.6 mm
X4373
Picking pin for streptomyces, tip diameter 1 mm
X4375
Picking pin for E.coli/phagemid, tip diameter 0.55 mm, deep well
X4376
Picking pin for Yeast picker+, tip diameter 1.6 mm
X4377
Picking pin for Yeast picker+, tip diameter 1.6 mm, deep well
X4378
Picking pin for yeast, tip diameter 1.6 mm, deep well
X4379
Picking pin for streptomyces, 1 mm, deep well
X4380
Picking pin for Phage picker+, tip diameter 1.6 mm, deep well
X4390
Picking Spring
X4451
Petri tray holder, 4 Hole
X4452
Petri Tray holder, 1 Hole
X4453
Petri Tray holder, 5 Hole
X4454
Omni Tray holder, 2 hole
X6023
Vented QTray with cover, 242 x 240 x 20 mm
X6029
Vented QTray with cover & 48 Well Divider, 242 x 240 x 20 mm
ME4541 Wash Bath
ME4542 Wash Brushes
Replacement Fuses
Fuses should only be replaced with the correct type and rating as specified:
• Input - F1 - T10A/250V - QPix 420/Halogen Heater
• Output - F2 - T5A/250V - Computer and Monitor
For more information, see Technical Specifications on page 173.
5026152 A
171
Replacement Parts and Optional Extras
172
5026152 A
B
Technical Specifications
Table B-1: External Dimensions and Weight
Size
1440 mm (width)
790 mm (depth)
780 mm (height)
Weight
QPix 420 System - 184 kg
Table (including compressor) - 165 kg
Table B-2: Compressed Air Supply
Minimum Pressure
100 psi
Maximum Pressure
120 psi
Minimum Volume
80 L/min
Table B-3: Operating Environment
Indoor Use Only
Temperature
10°C to 40°C
Humidity
20 to 80% non-condensing
Altitude
Up to 2000M
Mains Supply
+/- 10% Rated Voltage
Transient overvoltage
Installation Category (Overvoltage category) II
Rated Pollution
Pollution degree 2
Table B-4: European Electrical Supply
Voltage
230V AC 50 Hz single phase
Power
QPix 420 System - 1250W
Connections
IEC Input - QPix 420 Mains / Halogen Heater
IEC Output - PC and Monitor
Fuses
Input F1 - T10A / 250V - QPix 420/Halogen Heater
Output F2 - T5A / 250V - Computer and Monitor
Compressor
5026152 A
230V AC 50Hz 3.4A
173
Table B-5: North American Electrical Supply
Voltage
115V AC 60 Hz single phase
Power
QPix 420 System - 1250W
Connections
IEC Input - QPix 420 Mains
IEC Output - PC and Monitor
Fuses
Input F1 - T10A / 250V - QPix 420/Halogen Heater
Output F2 - T5A / 250V - Computer and Monitor
Compressor
115V AC 60Hz 7.5A
Electrical Connections
1
3
2
Figure B-1: QPix 420 Instrument Electrical Connections Panel
Item
Description
1
Mains Inlet
2
Robot (10A) & Monitor and PC (5A) Fuse holders
3
Computer and Monitor Outlets
WARNING! Ensure that all mains leads used by the QPix 420 System
meet specified power requirements appropriate for country of use.
Ensure that all equipment is suitably earthed.
Ensure mains plug is easily accessible when installed as this is the
disconnecting device.
The mains lead must not exceed 3 metres in length.
174
5026152 A
WARNING! Be careful of the drive magnets. Do not place metal or
other items near the X and Y axis where the head moves.
CAUTION! MAGNETIC DEVICE. Keep magnetic storage devices or strips, such
as hard drives, credit cards, etc., away from the instrument covers.
Dimensions of the QPix 420 System
Figure B-2: Front View of the QPix 420 System
Figure B-3: Side View of the QPix 420 System
5026152 A
175
176
5026152 A
Electromagnetic Compatibility (EMC)
C
REGULATORY INFORMATION FOR CANADA
(ICES/NMB-001:2006)
This ISM device complies with Canadian ICES-001.
Cet appareil ISM est confomre à la norme NMB-001 du Canada.
ISM EQUIPMENT CLASSIFICATION (Group 1, Class A)
This equipment is designated as scientific equipment for laboratory use that
intentionally generate and/or use conductively coupled radio-frequency energy
for internal functioning, and are suitable for use in all establishments, other
than domestic and those directly connected to a low voltage power supply
network which supply buildings used for domestic purposes.
INFORMATION FOR THE USER (FCC NOTICE)
This equipment has been tested and found to comply with the limits for nonconsumer ISM equipment, pursuant to part 18 of the FCC Rules. These limits
are designed to provide reasonable protection against harmful interference in
a non-residential installation. This equipment generates, uses, and can radiate
radio frequency energy and if not installed and used in accordance with the
instructions, might cause harmful interference to radio communications.
However, there is no guarantee that interference will not occur in a particular
installation. If this equipment does cause harmful interference to radio or
television reception, which can be determined by turning the equipment off
and on, the user is encouraged to try to correct the interference by one or
more of the following measures:
• Reorient or relocate the receiving antenna.
• Increase the separation between the equipment and receiver.
• Connect the equipment into an outlet on a circuit different from that to
which the receiver is connected.
• Consult the dealer or an experienced radio/TV technician for help.
In order to maintain compliance with FCC regulations, shielded cables must be
used with this equipment. Operation with non-approved equipment or
unshielded cables is likely to result in interference to radio and TV reception.
The user is cautioned that changes and modifications made to the equipment
without the approval of the manufacturer could void the user's authority to
operate this equipment.
5026152 A
177
Electromagnetic Compatibility (EMC)
178
5026152 A
Technical Assistance and Troubleshooting
D
This chapter contains information and guidance regarding issues that may need
technical assistance or troubleshooting.
Technical Assistance
Molecular Devices® is a leading worldwide manufacturer and distributor of
analytical instrumentation. We are committed to the quality of our products
and to fully supporting our customers with the highest possible level of
technical service.
Our support web site, www.moleculardevices.com/support.html, has links to
technical notes, software upgrades, and other resources. If you do not find the
answers you are seeking, follow the links to the Technical Support Request
Form to send an email message to a pool of technical support representatives.
Please have the System ID number, System serial number, software version
number, and the System owner’s name available when you call.
For all service and support needs, please contact:
Global Customer Support Center
1-800-635-5577
To Inquire About a Service Plan
North America
1-408-747-3694 (fax)
[email protected]
Europe
+44 118 944 8001 (fax)
[email protected]
Key Service and Support Offices
North America
1-800-635-5577
Technical Support: [email protected]
Instrument Service: [email protected]
Europe
+44 (0) 118 944 8000
Technical Support: [email protected]
Instrument Service: [email protected]
You can also contact your local Molecular Devices office.
5026152 A
179
Technical Assistance and Troubleshooting
Troubleshooting
Table D-1: Common Problems
Problem
Possible Solution
Instrument will not start.
System not functioning
correctly
•
Computer will not start.
•
•
•
•
Check that main power switch is turned on at the wall, the
emergency stop button is pulled out, and the start button is
pressed.
Check fuses in mains input lead plug and instrument.
Power the System off and on again.
Check the power switch on the computer and the main power
switched is turned on at the wall.
Check fuse in electrical connections panel. For more information
on fuses, see Electrical Connections on page 174.
One or more of the axes
won’t move.
•
Check the main power switch is turned on and the start button is
pressed.
Drive System fails to home.
•
Ensure the door is closed. Manually move the head to the centre
of the instrument and retry the process.
UV light won’t turn on.
•
•
Check that bulb is not burned out.
Ensure door is closed correctly.
Lamp failure.
•
Check whether halogen bulbs need replacing.
Picking alignment incorrect.
•
Align the picking pin, check for any bent pins on head.
Pins bend when inoculating
in microplate wells.
•
Ensure microplate is aligned correctly towards both arrows in
plate holder. Ensure correct microplate, head, and spacer blocks
are installed.
Poor picking results.
•
Run camera alignment process and check for bent pins in picking
process.
Check head is securely fastened.
Check picking height is correctly set.
Check wash bash routines and levels.
Check air pressure is at 100 psi. Ensure colonies of an adequate
size are being picked (97% pick efficiency is expected with
colonies between 1-1.5mm).
Check size, roundness, axis ratio, and threshold parameters.
Call technical support to discuss.
•
•
•
•
•
•
Crashes during destinaton
well plates inoculation.
•
Ensure microplates are positioned the right way round in
holders, and with lids off.
Picking pins bending on edge •
of bioassay tray.
Check the agar volume setting, bioassay tray positioning, tray
holder positioning in the bed.
Door Open warning shows.
•
Check door is closed and locked.
Low air warning.
•
•
Check air pressure is at 100 psi.
Check air compressor is switched on.
Message indicating licence
expiring soon.
•
Send licence request file to Molecular Devices (.req) following
the software instructions.
Failed to connect to devices
error message.
•
If you have recently disconnected the computer from the
instrument, check Ethernet connections in both instrument and
computer are correct.
Check that the instrument is powered on.
Restart software.
•
•
Barcodes failing to be read
correctly.
180
•
•
Ensure barcodes are correctly positioned on the receptacle.
Ensure barcodes are of correct type (Barcodes compatible with
the barcode reader are code 39, code 93, and code 128).
5026152 A
Glossary of Terms
Barcode: Unique label for source and
Datum Point: Series of X, Y, Z coordinates that define a set position on
the QPix 420 System bed.
Destination Plate: 96-well or 384well microplate pre-filled with liquid
medium to collect picked colonies.
Halogen Dryer: Proprietary ultra-high
temperature dryer used for the Pin
Sanitise System.
during picking.
X Drive: QPix 420 axis running from
right to left.
Y Drive: QPix 420 System axis running
from back to front.
Z Drive: QPix 420 System axis running
vertically from high to low on the QPix
420 bed
Image Acquisition: Capturing of
images using pre-defined acquisition
options.
LED Intensity: QPix 420 System uses
LEDs for consistent and reliable
imaging. Adjust the intensity of the
LEDs to control image exposure from
the Acquisition tab.
Interior Light: Illuminates the interior
of the instrument. Can be activated or
deactivated at any time using the
Interior Light icon in the bottom right
corner of the screen. Interior Light is
not used for imaging and will
automatically switch off during imaging.
Picking Pins: Reusable stainless steel
tools used to collect colonies.
Process: Standard program for QPix
420 System to carry out a task such as
a series of similar experiments, or a
maintenance task.
Proximity Indicators: Red lines
between colonies on the image that
show the nearest neighbour for each
colony. Note: This feature is not the
same as the colony exclusion feature in
Groups.
Receptacle: QTray or Petri dishes
containing colonies for picking.
Routine: QA specific type of process.
Transillumination: White light option
normally used to detect colonies using
LEDs positioned on the QPix 420
System head.
White Light: Full spectrum LED
illumination, used for configuring the
QPix 420 and for visualising colonies
5026152 A
181
Glossary of Terms
182
5026152 A
Index
A
adding and removing sample trails 168
adding tags to a location 162
adding tags to a receptacle 162
adding tags to a routine 162
additional display options - regional picking,
viewing 102
aligning the camera 47
annotations 164
annotations, adding 164
assistance, technical 179
B
barcode list, generate 68, 145
barcode reading options, selecting 67, 87, 109,
124, 134, 144
barcodes 67, 87, 109, 144, 160
barcodes window 19, 25
barcodes, generating random 68, 109, 145
barcodes, reading 124
barcodes, searching by 160
biological safety 12
C
camera alignment 44
change head 45
changing the head 48
chemical safety 12
cleaning 12
automated cleaning routine 56
colonies 80, 118
colonies, selecting 78, 98, 116
5026152 A
conducting a control plate creation routine
control plate creation settings summary 112
edit destination microplate 110
selecting barcode reading options 109
selecting head and sanitise options 32, 110
setting control plate creation source 111
setting destination options 109
conducting a gridding routine
creating a filter design layout 147
field patterns 147, 151
gridding settings summary 155
selecting destination tray 152
selecting head and sanitise options 146
selecting stamping and inking options 153
spot patterns 147
conducting a picking routine
deposit strategy 70
edit destination microplate 70
picking settings summary 73
setting destination options 69
setting filter pairs 69
setting picking source 72
conducting a rearraying routine
creating and editing a rearraying routine 133
defining destination receptacle 137
identifying source receptacle 135
preparing for a rearraying routine 133
viewing rearraying progress 141
viewing settings summary 41, 140
conducting a regional picking routine
configuring destination microplates 89
creating and editing a regional picking
routine 86
defining destination and source options 91
preparing for a regional picking routine 85
setting filter pairs 89
setting your regional picking source 90
viewing settings summary 94
183
Index
conducting a sanitise 60
conducting a UV sanitise 60
confirming holder layout 138
control plate creation progress, viewing 120
control plate creation routine, conducting 108
control plate creation routine, creating and
editing 108
control plate creation settings summary,
viewing 112
control plate creation source 111
control plate creation source, setting 111
control plate creation, preparing 107
creating and editing a control plate creation
routine 108
creating and editing a gridding routine 143
creating and editing a picking routine 66
creating sanitise profiles 61
creating tags 162
D
data search, conducting 159
data viewer processes 42
adding annotations 164
adding or deleting microplate properties 165
conducting data search 159
exporting processes 165
exporting routines 165
removing a tag 163
search by barcode 160
search by date 161
search by location 161
search by tag 160
search by user 161
viewing and printing settings details 161
viewing locations maps 167
working with sample trails 168
working with tags 162
database management 42
dates 161
dates, searching by 161
defining destination receptacle 137
definitions
warning and wautions 9
deleting a sanitise profile 63
deposit strategy 70
184
destination microplate, editing 70, 110
destination microplates, configuring 89
destination options 91
destination options window 25
destination options, setting 109
destination receptacle, defining 137
destination tray, selecting 152
destination window (rearraying) 39
destination/source options window (regional
picking only) 26
detination options, setting 69
display icons 55
display options tab 30, 81, 118
display options, viewing 81, 118
E
editing sanitise profiles 61, 62
electrical connections 174
electrical safety 11
electromagnetic compatibility 177
EMC 177
emergency stop 13
F
feature counts tab 30, 80, 118
feature selection window 29
field patterns 147, 151
filter design layout, creating 147
filter layout window 152
filter pair and barcodes 87
filter pairs 67, 87
filter pairs list 24
filter pairs, setting 69, 89
fluorescent light test image, creating
fluorescent light test image, regional picking
98
fluorescent only, filter pairs 89
fluorescent test image window 29
fluorescent test image, creating 77
fluroescent light only 77
5026152 A
G
M
general precautions 9
generate barcode list 68, 145
generate random barcodes 68, 109, 145
gridding progress, viewing 157
gridding routine, creating and editing 143
gridding settings summary, viewing 155
gridding, conducting 143
gridding, preparing 143
maintenance
annual 55
cleaning 12
general 55
general precautions 9
instrument 9
service 55
weekly 55
manage sanitise profiles 43
microplate and sanitise options 127
microplate and sanitise options, setting 127
microplate properties, adding and deleting 165
microplates, loading 103
microplates/sanitise window 35
moving parts 12
H
head and sanitise options, selecting 138
head and sanitise window 39
head options 32, 71, 92, 110, 146
head options, setting 128
head window 36
head/sanitise window 26
health and safety 10
picking progress, viewing 82
holder layout - replicating, confirming 128, 154 picking routine, completing 105
holder layout summary 74, 95
picking routine, conducting 66
holder layout summary window 22, 28, 34
picking routine, creating and editing 66
holder layout, confirming 138
picking routine, preparing 65
holders, arranging layout 74
picking settings summary, viewing 73
picking source 72
picking source, setting 72
pin fire test 45, 49
plate holders, loading 82, 119
power-up procedures 51
inoculation heights 71, 110
preparing for a control plate creation routine
instrument dimensions 175
107
instrument maintenance 9
preparing for a gridding routine 143
preparing for a picking routine 65
pre-power-up procedure 51
procedures
power-up 51
load plates window 22, 30, 34, 36, 40
pre-power-up 51
shutdown 52
loading plate holders 82, 119
processes, exporting 165
location 161
location, adding tags 162
location, searching by 161
locations map, show 167
locations maps, viewing 167
P
I
L
5026152 A
185
Index
running a gridding routine
continuing or saving routine 156
viewing picking progress 157
running
a picking routine
reading barcodes 134
arranging layout of the holders 74
rearraying processes overview 38
completing routine 83
rearraying progress, viewing 141
rearraying routine, creating and editing 133
creating a fluorescent test image 77
rearraying settings summary, viewing 41, 140
creating a white light test image 75
rearraying source receptacle, identifying 135
loading plate holders 82, 119
rearrraying routine, preparing 133
selecting colonies 78
receptacle, adding tags 162
viewing display options 81
regional picking 85
display options tab 30
viewing selected colonies 80
regional picking destination and source options, running a rearraying routine
defining 91
confirming the holder layout 138
regional picking head and sanitise options,
running a regional picking routine 95
selecting 92
arranging holders 95
regional picking overview 24
completing picking routine 105
regional picking progress, viewing 104
creating fluorescent light test image 98
creating white light test image 96
regional picking routine, creating and editing 86
loading microplates 103
regional picking routine, preparing 85
saving your routine 103
regional picking settings summary, viewing 94
removable parts
viewing additional display options - regional
head 57
picking 102
replicating process overview 35
viewing progress 104
replicating routine, preparing 123
viewing selected regional colonies 101
replicating routine, saving 130
running a replicating routine
replicating routing, creating and editing 124
confirming holder layout 128, 154
routine, adding tags 162
creating and editing a replicating routine 124
routine, continuing or saving 81, 119, 156
preparing for replicating 123
routine, rearraying 133
saving routine 130
routine, saving 103
routines
setting head options 128
aligning the camera 47
setting microplate and sanitise options 127
changing the head 48
viewing settings summary 130
pin fire test 49
routines window 19, 24
routines, exporting 165
running a control plate creation routine
safety
control plate creation, running 113
biological 12
creating an image 114
chemical
12
electrical
11
viewing display options 118
emergency stop button 13
features 13
viewing selected colonies 118
health 10
moving parts 12
R
S
186
5026152 A
Index
safety and health 10
safety features 13
sample trails, adding or removing 168
sample trails, editing 168
sample trails, viewing and deleting 168
sample trails, working with 168
sanitise options 32, 71, 92, 110, 146
sanitise options, selecting 138
sanitise profiles, creating 61
sanitise profiles, deleting 63
sanitise profiles, editing 61, 62
sanitise window 46
selected colonies, regional picking 101
selected colonies, viewing 80, 118
selected regional colonies, viewing 101
selecting barcode reading options 124, 134
selecting colonies 78, 98, 116
selecting head and sanitise options, rearraying
138
service and maintenance 55
setting head options 128
setting source and destination receptacles 146
setting summary window (replicating) 37
setting up routines
conducting a sanitise 60
conducting a UV sanitise 60
creating and editing sanitise profiles 61
deleting a sanitise profile 63
editing a sanitise profile 62
settings details, viewing and printing 161
settings summary - replicating, viewing 130
settings summary window (picking) 27
show locations map 167
shutdown procedure 52
single and multi-dipping, multi-dip, single and
multi 70, 109
187
software overview
barcodes window 19, 25
camera alignment 44
change head 45
current and new processes 18
data viewer processes 42
database management 42
destination options window 25
destination window (rearraying) 39
destination/source options window (regional
picking only) 26
display options tab 30
feature counts tab 30
feature selection window 29
filter pairs list 24
fluorescent test image window 29
head and sanitise window 39
head window 36
head/sanitise window 26
holder layout summary 22, 28, 34
instrument utilities 45
load plates window 22, 30, 34, 36, 40
manage sanitise profiles 43
menu options 18
micorplates/sanitise window 35
navigation window 17
pin fire test 45
rearraying processes overview 38
replicating process overview 35
routines window 19, 24
sanitise window 46
settings summary (replicating) 37
settings summary window (picking) 27
source window 27
source window (rearraying) 38
standard and regional picking 24
test image window 28
UV santise window 46
source 90
source and destination microplates and filters,
setting 146
source options 91
source receptacle, rearraying 135
source window 27
source window (rearraying) 38
source, setting regional picking 90
spot patterns 147
stamping and inking options, selecting 153
standard picking overview 24
5026152 A
Index
substrate window 153
T
tags 160, 162, 163
tags, creating 162
tags, removing 163
tags, searching by 160
tags, working with 162
technical assistance 179
technical specifications 173
dimension of the instrument 175
electrical connections 174
test image window 28
test image, creating 114
U
users 161
users, searching by 161
UV sanitise window 46
V
viewing and deleting sample trails 168
viewing rearraying progress 141
viewing rearraying settings summary 41, 140
W
warning and caution definitions 9
WEEE compliance 11
white light test image, creating 75, 96
white light test image, regional picking 96
188
5026152 A

QPix 420 Colony Picking System User Guide

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