Macros for Fiji/ImageJ
This macro generates colorized images, merged channels and create stacks from images acquired with the IN Cell Analyzer 2200 (Cytiva, USA).
1 - Download this zip file and extract the IN_Cell_Analyzer_2200_Manipulator.ijm file to the plugins'
subfolder of Fiji main folder (Fiji.app > plugins). If Fiji is open, restart it.
2 - Select Plugins > IN Cell Analyzer 2200 Manipulator. It will likely be one of the last options. Alternatively, you can search for the macro in Fiji's search bar and click
Run.
3 - Select the main folder where images are located. This macro will also run automatically on each and every subfolder located within this main folder.
4 - Select number of channels acquired (2, 3 or 4) and click OK.
5 - Next, you will select the order of channels in the stack with respect to the acquisition order. In this example, the acquisition order was DAPI (1) and FITC (2).
If you want to keep that order in the stack you should type 1,2. In this case I wanted to alter the order in the stack to FITC (1) and DAPI (2), so I typed 2,1. Make sure to include a comma between the numbers. Next, you will atribute a color to each of the channels and the click OK.
6 - The macro will start running. A log window will pop up and update after every file gets processed, showing the % of files already processed and an estimated time to process all files.
7 - After all files were processed, the log window will display the elapsed time. The processed images will be stored within the manipulator_processed_images folder located within very processed subfolder.
8 - Within every manipulator_processed_images folder there will be three subfolders, named colorized, merge and stack, which respectively stores colorized images,
merged channels and stacks.
If you use this macro to generate data for a publication, please cite it by using the following link: https://github.com/iuri-cv/fiji_macros/blob/main/IN_Cell_Analyzer_2200_Manipulator.ijm
If you have any questions, suggestions or criticisms about this macro, please contact me at [email protected]. Any feedback will be highly appreciated 😀