User has to click OK to allow macro to progress to window for coordinate input.Ĭhanged the way the macro handles the random square coordinates. Macro waits for user to copy and save the ROI coordinates, and generate the random square coordinates. 'ROI selection from coordinates' ImageJ macroĪdded function to create the folder tree if not already present.Īdded function to launch Recorder and change cursor to Polygon Selection. The Python scripts should be usable once Python for Windows is installed.Ĭompared to previous version, added global variables for ImageJ macros to easily change Parent directory, number of random squares analysed and size of the squares across the various ImageJ macros.Ĭhanged repeating macro variables to be able to handle 10 or more squares.
#Imagej particle counting install
ijm file and the Hull And Circle.jar file into ImageJ and it should install itself. To install the ImageJ macro, just drag and drop the. *This can of course be adjusted to your preference, but that also means changing the the folder tree format in all macros according to your preference too. tif/tiff images MUST* be named in this format (without the brackets): To use the ImageJ macros and scripts, a prerequisite is that your 'Whole region'. Under the #Variables heading, change the Installation location of 7-Zip if necessary. NUMBER_OF_POINTS and SQUARE_WIDTH: Adjust to correspond with No_squares and Square_size in Particle_analyses_macro.ijmįilter Particle Diameter Python script (Filter_Particle_Diameter.py):
#Imagej particle counting generator
Random coordinate generator Python script (Random_Coordinates.py): Again, this needs to be optimised depending on the amount of total area available for analysis. Square_size: Adjust the size of the squares to be generated and analysed. May need to be optimised based on the amount of total area available for analysis. No_squares: Adjust the number of squares intended to be generated and analysed accordingly. You can also change this to your 'test' folder for optimisation of parameters. I recommend this to be a dedicated folder for your analysis. Parent_folder: Change the directory to where you want the generated random squares to be saved.
ImageJ macro (Particle_analyses_macro.ijm): Hull And Circle (3rd party plugin for ImageJ, included)Īdjust the global variables within each macro/Python script as necessary:
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