This is a system to help you in ImageJ macro writing.
It gives a structure in five parts to your code, provides code for all input/output, and code for some usefull functions.
You will be ask to choose some blocks of functions you need in your ImageJ macro and the generator will produce a code that you can directly paste into a txt file and run as a macro file with ImageJ.
For some blocks (as indicated) you need to adapt the code to your needs, so some basic knowledge of ImageJ macro writting is needed.
The code was done with ImageJ 1.47f, you may find some incompatibility. Please tell me if it is the case.
Fabrice Duprat:duprat@ipmc.cnrs.fr
Visit my web site !
January 2015
(a code sequence is in the last line of the previously generated macro)
Name of the macro Date of last modification Author Email ImageJ Version Short description INPUT: Describe the image type (one color image, a directory with 16 bits stacks, …) and what the macro is expecting you to do (used objective, …) OUTPUT: Describe what the macro is producing (graphs, excel file, images, ….)
Name of the macro
Date of last modification
Author
Email
ImageJ Version
Short description
INPUT: Describe the image type (one color image, a directory with 16 bits stacks, …) and what the macro is expecting you to do (used objective, …)
OUTPUT: Describe what the macro is producing (graphs, excel file, images, ….)
Close all opened images Clear the Results window Close the Log window Close the ROI Manager window
Close all opened images
Clear the Results window
Close the Log window
Close the ROI Manager window
Set some variables and ImageJ parameters (you must adapt the code to your needs)
Example of dialog box for parameters imput (you must adapt the code to your needs) Change the scale according to the choosen objective (need to select the above dialog box and must adapt the code to your needs)
Example of dialog box for parameters imput (you must adapt the code to your needs)
Change the scale according to the choosen objective (need to select the above dialog box and must adapt the code to your needs)
How many image(s) are analysed in each run of the macro One image Two images Three images (ex: 2 images if you need to subtract one to another in your analysis)
How many image(s) are analysed in each run of the macro One image Two images Three images
(ex: 2 images if you need to subtract one to another in your analysis)
SELECT ABOVE THE NUMBER OF IMAGES AND CLICK ON CHOOSE BUTTON
Give hand to adjust threshold and create a mask, save the default threshold values (you must adapt the code to your needs) Modifying the mask before analysis Crop the image from a ROI Select a ROI and subtract its mean value (ex: background subtraction). Beware this code clear the results window. Make a selection from a complex shape and modify the points
Give hand to adjust threshold and create a mask, save the default threshold values (you must adapt the code to your needs)
Modifying the mask before analysis
Crop the image from a ROI
Select a ROI and subtract its mean value (ex: background subtraction). Beware this code clear the results window.
Make a selection from a complex shape and modify the points
IMPORTANT:
Always replace the used Image1 title by the variable my_title_image1 in the following lines
(Instead you can choose to end the loop after the measurements conditionning or after exportation, see below)
Extract selected measurements from Results window, store as a table in Log window (you must adapt the code to your needs) Extract selected measurements from Results window and store it in an array (you must adapt the code to your needs) Copy measurements from arrays into Results window (you must adapt the code to your needs) Copy measurements from arrays into Log window (you must adapt the code to your needs)
Extract selected measurements from Results window, store as a table in Log window (you must adapt the code to your needs)
Extract selected measurements from Results window and store it in an array (you must adapt the code to your needs)
Copy measurements from arrays into Results window (you must adapt the code to your needs)
Copy measurements from arrays into Log window (you must adapt the code to your needs)
(Instead you can choose to end the loop after analysis, see above, or after exportation, see below)
Ask too create a new subdirectory in the image directory (you must adapt the code to your needs) Save the Results window as text file Save the Log window as text file
Ask too create a new subdirectory in the image directory (you must adapt the code to your needs)
Save the Results window as text file
Save the Log window as text file
(Instead you can choose to end the loop after analysis or after conditionning, see above)