Course 4 –
Advanced Image Analysis & Processing
April 2015
1
From Survey Results
• Heterogenous audience
• Day 1 : ImageJ -Macro : language, batch, use of
ActionBar.
• Day2 : ImageJ - Plugins : install, writing, use of
Eclipse.
• Day 3 : Matlab & CellProfiler, how to use them for
image analysis, comparison to ImageJ
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Fiji
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Fiji
Plugins
http://fiji.sc/Fiji
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Get Action Bar Plugin
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Add Action Bar Plugin
Fiji.app\plugins
Paste :
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Add Action Bar Plugin
Fiji.app\plugins
Paste :
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My first Action Bar
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My first Action Bar
Fiji.app\plugins\ActionBar
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My first Action Bar
Refresh Menus
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My first Action Bar
Fiji.app\plugins\ActionBar
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My first Action Bar
Create
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My first Action Bar
Paste
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Change
File
Format
Colored text
easier to debug
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Not Saved
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Save Your Action Bar
My_Action_Bar.ijm
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Action Bar
basic functions
…
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Action Bar
basic functions
…
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Action Bar
change Icon
New icon file name
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Action Bar
change Icon
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Action Bar
change Label
label
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Action Bar
change Label
label
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Action when clic on button
Clic
Action
to perform
//using macro functions
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Macro Functions
Website
Recorder
OR
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Macro Functions
Website
Recorder
OR
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Record Functions
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Record Functions
Macro language
RGB
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Record Functions
Action
to perform
// start of : line
//using macro functions
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end
start
of the button line
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Use a macro :
on an image
DAPI
EdU-488
H2B-RFP
Create a macro to
analyse Red and Green
staining.
Create a nuclei mask from DAPI
Get for each nuclei :
- the «Area»
and
- the «Intensitiy» of the Red and
Green Channel
You have 30min!
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How to write a macro
Template: tiny.cc\adip-1stStepMacro_blank
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How to write a macro
Solution : tiny.cc\adip-1stStepMacro
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Use a macro :
on a folder
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Use a macro :
on a folder
Process>Batch>Macro
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Use a macro
on a folder
Process>Batch>Macro
Necessary to handle the processing of several images
Solution : tiny.cc\adip-2ndStepMacro
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Use a macro
on a folder
Process>Batch>Macro + GUI for parameters
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Use a macro
on a folder
Process>Batch>Macro + GUI for parameters
• How to ask user to set/select parameters
Starts with : Dialog.create();
Website
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Use a macro
on a folder
Process>Batch>Macro + GUI for parameters
Solution : tiny.cc\adip-3rdStepMacro
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Use a macro
on a folder
Process>Batch>Macro + GUI for parameters
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Use a macro
on a folder
Process>Batch>Macro + GUI for parameters
How to specify the parameters once and use them for all images ?
40
Use a macro
on a folder
Macro: process image of a folder
• Keep the same Macro
• Modify it so it can process every file in a folder!
• You will need:
– The path of the folder containing images.
– The list of the files.
• You will have to :
– Create a new folder to save images (mask)
– Process every file.
– Save the created mask of every image.
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Use a macro
on a folder
Macro: process image of a folder
• Keep the same Macro
• Modify it so it can process every file in a folder!
• You will need:
– The path of the folder containing images. getDirectory
– The list of the files. getFileList
• You will have to :
– Create a new folder to save images (mask) …
– Process every file …
– Save the created mask of every image …
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Use a macro
on a folder
Macro: process image of a folder
…
…
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Use a macro
on a folder
Macro: process image of a folder
…
What happens if :
there is non-image File within the folder?
…
To prevent issue, we’ll use a function
to control that files are images.
Solution : tiny.cc\adip-4thStepMacro
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Use a macro
in a Action Bar!
Macro: process image of a folder
We can use our own <macro> code
//using macro functions
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Use a macro
in a Action Bar!
on 1 image
We can use our own <macro> code adip-1stStepMacro.ijm
Solution : tiny.cc\MyImproved_action_bar_step1.ijm
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Use a macro
in a Action Bar!
on 1 folder
We can use our own <macro> code adip-4thStepMacro.ijm
…
Solution : tiny.cc\MyImproved_action_bar_step2.ijm
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Use a macro
in a Action Bar!
on 1 folder
We can use our own <macro> code adip-4thStepMacro.ijm
…
This function can be necessary
for other buttons of the Action Bar
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Use a macro
in a Action Bar!
codelibrary
<codeLibrary> contains functions that every <button> can access
Which other functions can we add to the <codeLibrary> ?
Solution : tiny.cc\MyImproved_action_bar_step3.ijm
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Use a macro
in a Action Bar!
codelibrary
the common part when processing
1 image and 1 folder
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Use a macro
in a Action Bar!
codelibrary
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Use a macro
in a Action Bar!
codelibrary
Solution : tiny.cc\MyImproved_action_bar_step4.ijm
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Use a macro
in a Action Bar!
Parameters Windows : function
• We need to:
– Store data (text, numbers…)
– Retrieve these data
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Use a macro
in a Action Bar!
Parameters Windows : function
Container will be an ImageJ text window
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Use a macro
in a Action Bar!
Parameters Windows : function
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Use a macro
in a Action Bar!
Parameters Windows : function
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Use a macro
in a Action Bar!
Parameters Windows : modify action bar
Retrieve data
Set them first !
Solution : tiny.cc\MyImproved_action_bar_step5-0.ijm
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Use a macro
in a Action Bar!
Parameters Windows : setData
Set Parameters <button>
Solution : tiny.cc\MyImproved_action_bar_step5-1.ijm
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Use a macro
in a Action Bar!
Parameters Windows : setData
Use it for the Folder <button>
Solution : tiny.cc\MyImproved_action_bar_step5.ijm
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That’s all Folks!
Tomorrow : JaaavvaaaAAAArrrgggghhh
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