course 4 advanced image analysis & processing · 2018-04-12 · advanced image analysis &...
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Course 4 –Advanced Image Analysis & Processing
April 2015
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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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FijiPlugins
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http://fiji.sc/Fiji
Get Action Bar Plugin
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Add Action Bar Plugin
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Fiji.app\plugins
Paste :
Add Action Bar Plugin
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Fiji.app\plugins
Paste :
My first Action Bar
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My first Action Bar
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Fiji.app\plugins\ActionBar
My first Action Bar
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Refresh Menus
My first Action Bar
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Fiji.app\plugins\ActionBar
My first Action Bar
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Create
My first Action Bar
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Paste
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ChangeFile
Format
Colored texteasier to debug
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Not Saved
Save Your Action Bar
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My_Action_Bar.ijm
Action Barbasic functions
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…
Action Barbasic functions
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…
Action Barchange Icon
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New icon file name
Action Barchange Icon
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Action Barchange Label
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label
Action Barchange Label
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label
Action when clic on button
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Clic
Actionto perform
//using macro functions
Macro Functions
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Recorder Website
OR
Macro Functions
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OR
Recorder Website
Record Functions
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Record Functions
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RGB
Macro language
Record Functions
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Actionto perform
//using macro functions
// start of : line
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of the button lineendstart
Use a macro : on an image
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DAPI
H2B-RFPEdU-488
Create a nuclei mask from DAPI
Get for each nuclei :- the «Area» and - the «Intensitiy» of the Red and Green Channel
Create a macro to analyse Red and Green staining.
You have 30min!
How to write a macro
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Template: tiny.cc\adip-1stStepMacro_blank
How to write a macro
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Solution : tiny.cc\adip-1stStepMacro
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
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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 ?
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• 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.
Use a macro on a folder
Macro: process image of a folder
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• 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 …
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
…
…
…
…
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What happens if : there is non-image File within the folder?
To prevent issue, we’ll use a functionto control that files are images.
Use a macro on a folder
Macro: process image of a folder
Solution : tiny.cc\adip-4thStepMacro
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Use a macro in a Action Bar!
Macro: process image of a folder
//using macro functions
We can use our own <macro> code
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Use a macro in a Action Bar!
on 1 image
adip-1stStepMacro.ijmWe can use our own <macro> code
Solution : tiny.cc\MyImproved_action_bar_step1.ijm
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Use a macro in a Action Bar!
on 1 folder
adip-4thStepMacro.ijmWe can use our own <macro> code
…
Solution : tiny.cc\MyImproved_action_bar_step2.ijm
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Use a macro in a Action Bar!
on 1 folder
adip-4thStepMacro.ijmWe can use our own <macro> code
This function can be necessaryfor other buttons of the Action Bar
…
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Use a macro in a Action Bar!
codelibrary
contains functions that every <button> can access<codeLibrary>
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 processing1 image and 1 folder
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Use a macro in a Action Bar!
codelibrary
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Solution : tiny.cc\MyImproved_action_bar_step4.ijm
Use a macro in a Action Bar!
codelibrary
• We need to:– Store data (text, numbers…)– Retrieve these data
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Use a macro in a Action Bar!
Parameters Windows : function
Use a macro in a Action Bar!
Parameters Windows : function
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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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Set them first !
Retrieve data
Use a macro in a Action Bar!
Parameters Windows : modify action bar
Solution : tiny.cc\MyImproved_action_bar_step5-0.ijm
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Use a macro in a Action Bar!
Parameters Windows : setData
Solution : tiny.cc\MyImproved_action_bar_step5-1.ijm
Set Parameters <button>
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Use a macro in a Action Bar!
Parameters Windows : setData
Solution : tiny.cc\MyImproved_action_bar_step5.ijm
Use it for the Folder <button>
That’s all Folks!
Tomorrow : JaaavvaaaAAAArrrgggghhh
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