1. No category

A CellProfiler introduction
BIOP-EFPL
2015
1
Welcome
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OPEN RGB IMAGE
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Select an image
Drag and Drop the image:
test_RGB .tif
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Output Folder
View Output settings
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Specify output folder
Metadata
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NamesAndType
Select Color Image
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Groups
Leave Default
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Start Test Mode
Start Test Mode
Error window pops-up
The module list is empty…
Adjust modules : +
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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
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Module
An image window pops-up
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Module
Change Names
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Module
GrayToColor
Select Images
Start Test Mode
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Module
Default display RGB
Reordered color after import
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OPEN A COMPOSITE IMAGE
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Open a composite image
reUse RGB opening
Drag and Drop the image:
test_3channels .tif
Start Test Mode
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Issue!
Composite images are not handled as RGB
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Open a composite image
set : Metadata
Extract MetaData : YES
Metadata extraction method : extract from image file headers
Select Update metadata
Update
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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
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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
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Open a composite image
set : NamesAndTypes
Delete ColorToGray.
Not necessary anymore
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Start Test Mode
Open a composite image
set : NamesAndTypes
An image window pops-up
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IDENTIFY PRIMARY OBJECTS
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Identify Primary Objects
Default Parameters
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Identify Primary Objects
Default Parameters
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Identify Primary Objects
Change Threshold strategy to ‘’Global’’
Change to Global
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Identify Primary Objects
Change Threshold strategy and compare
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Change Class Thresholding
to Three classes
Change to Three classes
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Change to three classes
and compare
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Change middle class assignment
to background
Change to Background
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Change middle class assignment
to background
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Clumped objects
Change to Shape
Compare Intensity,Shape,Porpagate
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Clumped objects
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Clumped objects
Size of smoothing
Distance between local maxima
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Clumped objects
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Measures Intensity
using objects
Select an Image Edu
Add another Image and select the image RFP
Select the Object to use for the measure
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Export Measures
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Measures
Measurements Selection
Select the measurements to export :
change to YES .
Select the Object to use for the measure.
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Measures
Measurements Selection
Select measurements window pops-up.
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Save an ‘‘Ouput’’ image
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Save 2 ‘‘Ouput’’ images
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Save 2 ‘‘Ouput’’ images
Append a suffix : Change to YES
Specify a text
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SECONDARY OBJECT
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Secondary object
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Issue !
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Outlines
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Outlines
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Measure intensities
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Save “Output”Images
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TERTIARY OBJECTS
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Tertiary objects
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CSV OUTPUT FILE
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Data that we want
What do we have?
Numbers
What do we want?
Graphics and little stars
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Data that we have
MyExpt_NucleiObject.csv
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Data that we want
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Data that we want
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Data that we have
MyExpt_NucleiObject.csv
MyExpt_Image.csv
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Data that we have
MyExpt_NucleiObject.csv
MyExpt_Image.csv
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Data that we have
MyExpt_NucleiObject.csv
MyExpt_Image.csv
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Data that we have
MyExpt_NucleiObject.csv
MyExpt_Image.csv
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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
)
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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)
)
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Crossing values from different tables
formula
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Extracting informations from ImageName
Insert a column
Copy
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Extracting informations from ImageName
Paste value
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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
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Extracting informations from ImageName
Column are filled with informations
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Table
create one
Select the whole table (mouse or Ctl+A)
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Table
create one
Select Insert
Create Table window pops-up
Select Table
Select OK
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Table
create one
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Pivot Table
create one
Select Pivot Table
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Pivot Table
create one
Select OK
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Pivot Table
getting started
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Pivot Table
getting started
Click in that field
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Pivot table
getting started
To have access to column
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Pivot Table
getting started
Select ImageName, in Rows
Select Intensity_mean… ,
in Values,
Change Sum to Average
(click, Value Field Settings)
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Pivot Table
getting more
Change to Edu et RFP status
…and ImageReplicate
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Pivot Table
getting more
Insert
Graph Bar
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Pivot Table
getting more
You get an interactive graph!
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