Image Processing with Cell Profiler

A CellProfiler introduction
BIOP-EFPL
2015
1
Welcome
2
OPEN RGB IMAGE
3
Select an image
Drag and Drop the image:
test_RGB .tif
4
Output Folder
View Output settings
5
Specify output folder
Metadata
6
NamesAndType
Select Color Image
7
Groups
Leave Default
8
Start Test Mode
Start Test Mode
Error window pops-up
The module list is empty…
Adjust modules : +
9
Module
The «Add modules» window
pops-up.
In module categories:
- select ‘’Image Processing’’
Then :
- double-clic ‘’ColorToGray’’
ColorToGray appears in the ‘’Analysis modules’’ list
Select the input image,
Set ‘’Conversion method’’ to ‘’ Split’’
Set Image type to ‘’RGB’’
Start Test Mode
10
Module
An image window pops-up
11
Module
Change Names
12
Module
GrayToColor
Select Images
Start Test Mode
13
Module
Default display RGB
Reordered color after import
14
OPEN A COMPOSITE IMAGE
15
Open a composite image
reUse RGB opening
Drag and Drop the image:
test_3channels .tif
Start Test Mode
16
Issue!
Composite images are not handled as RGB
17
Open a composite image
set : Metadata
Extract MetaData : YES
Metadata extraction method : extract from image file headers
Select Update metadata
Update
18
Open a composite image
set : NamesAndTypes
Assign a name to : Images matching rules
Select the rule
Metadata Does Have C matching 0
Name to assign these images : ex ‘’DAPI’’
Select the image type Grayscale image
Add another image
19
Open a composite image
set : NamesAndTypes
Assign a name to : Images matching rules
Select the rule : Metadata Does Have C matching 0
Name to assign these images : ex ‘’DAPI’’, ‘
Select the image type Grayscale image
…
Metadata Does Have C matching 1, / ‘’Edu’’,
Metadata Does Have C matching 2, / ‘’RFP’’,
Update
20
Open a composite image
set : NamesAndTypes
Delete ColorToGray.
Not necessary anymore
21
Start Test Mode
Open a composite image
set : NamesAndTypes
An image window pops-up
22
IDENTIFY PRIMARY OBJECTS
23
Identify Primary Objects
Default Parameters
24
Identify Primary Objects
Default Parameters
25
Identify Primary Objects
Change Threshold strategy to ‘’Global’’
Change to Global
26
Identify Primary Objects
Change Threshold strategy and compare
27
Change Class Thresholding
to Three classes
Change to Three classes
28
Change to three classes
and compare
29
Change middle class assignment
to background
Change to Background
30
Change middle class assignment
to background
31
Clumped objects
Change to Shape
Compare Intensity,Shape,Porpagate
32
Clumped objects
33
Clumped objects
Size of smoothing
Distance between local maxima
34
Clumped objects
35
Measures Intensity
using objects
Select an Image Edu
Add another Image and select the image RFP
Select the Object to use for the measure
36
Export Measures
37
Measures
Measurements Selection
Select the measurements to export :
change to YES .
Select the Object to use for the measure.
38
Measures
Measurements Selection
Select measurements window pops-up.
39
Save an ‘‘Ouput’’ image
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Save 2 ‘‘Ouput’’ images
41
Save 2 ‘‘Ouput’’ images
Append a suffix : Change to YES
Specify a text
42
SECONDARY OBJECT
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Secondary object
44
Issue !
45
46
Outlines
47
Outlines
48
Measure intensities
49
Save “Output”Images
50
TERTIARY OBJECTS
51
Tertiary objects
52
CSV OUTPUT FILE
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Data that we want
What do we have?
Numbers
What do we want?
Graphics and little stars
54
Data that we have
MyExpt_NucleiObject.csv
55
Data that we want
56
Data that we want
57
Data that we have
MyExpt_NucleiObject.csv
MyExpt_Image.csv
58
Data that we have
MyExpt_NucleiObject.csv
MyExpt_Image.csv
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Data that we have
MyExpt_NucleiObject.csv
MyExpt_Image.csv
60
Data that we have
MyExpt_NucleiObject.csv
MyExpt_Image.csv
61
Crossing values from different tables
formula
=INDEX (
)
Column_I_want_a_return_value_from ,
(
MATCH ( My_Lookup_Value , Column_I_want_to_Lookup_against , 0
)
62
Crossing values from different tables
formula
=INDEX (
)
= INDEX (
)
Column_I_want_a_return_value_from ,
(
MATCH ( My_Lookup_Value , Column_I_want_to_Lookup_against , 0
)
MyExpt_Image!$B$1:$B$9,
(
MATCH( MyExpt_NucleiObject!A2 , MyExpt_Image!$E$1:$E$9, 0)
)
63
Crossing values from different tables
formula
64
Extracting informations from ImageName
Insert a column
Copy
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Extracting informations from ImageName
Paste value
66
Extracting informations from ImageName
Select Column
Text to Column
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Extracting informations from ImageName
Select Other, and specify _
Select Delimited
Next
Next
68
Extracting informations from ImageName
Column are filled with informations
69
Table
create one
Select the whole table (mouse or Ctl+A)
70
Table
create one
Select Insert
Create Table window pops-up
Select Table
Select OK
71
Table
create one
72
Pivot Table
create one
Select Pivot Table
73
Pivot Table
create one
Select OK
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Pivot Table
getting started
75
Pivot Table
getting started
Click in that field
76
Pivot table
getting started
To have access to column
77
Pivot Table
getting started
Select ImageName, in Rows
Select Intensity_mean… ,
in Values,
Change Sum to Average
(click, Value Field Settings)
78
Pivot Table
getting more
Change to Edu et RFP status
…and ImageReplicate
79
Pivot Table
getting more
Insert
Graph Bar
80
Pivot Table
getting more
You get an interactive graph!
81