SegmeCount by Ryan M Lee
Tentative Description.
Automatic Cell Counter for use in ImageJ Fiji
Structure of Github repository:
Macrocode
~All version of the macro. Includes original macro and final macro, marked alonviruscounter and segmecount_final respectively.
testimages
~Contains raw image test files, along with the resulting counts and processed images.
Comparisons.xlsx
~Comparisons between each version of the Macro Codes
README.md
~This file.
V5 Vs V7 Comparison Counts.xlsx
~Using a larger set of data, comparison of processed values between the V5 and the V7.
counter.py
~Program to open one directory and compile each .csv count file along with the file name into a single file.
Procedure:
- Utilize any imaging program for your sample data, and name the files appropriately. I would recommend utilizing .tif files due to their versatility in image processing.
- Using the imaging program, measure the scale of the image. For example, how much is 10 pixels equivalent to?
- Open ImageJ Fiji, or install if not already. Go to Plugins/Macros/Edit, and select segmecount_final.ijm from wherever it was placed on your file system.
- Go to line 27, and change the scale values. In the original code, it is noted to be 222.6 micrometers per 10 pixels.
- If you know the range of size thresholds for your image, please refer to lines 55 and 56 and change the thresholds to your liking, in micrometers squared.
- Run the Macro from the current screen. (Edit screen). Select your largest directory containing all the files you wish to count.
- After the macro finished running, open counter.py. On the bottom, where it notes "directory_path = "/Users/orphanlab/Downloads/240829_Counts"", please change this to the path of your largest directory from step 6.
- Run counter.py, and you will obtain a cellcounts.csv file with the associated paths of each file and the number of cells.