A Fiji macro written in jython to analysis IF images of cyrosection from organoid tissues.
We provide analysis 4 (or more) channels IF of histology sections of organoids. Written for midbrain organoid images.
This is a macro written in Jython for Fiji (ImageJ) you must use Fiji because some Pull program into Fiji and press run. To see the images and optimize settings set 'batch mode = FALSE'
You will be asked to select your input folder. This will contain images of organoids to quantify. Select your output folder.
The results will be a csv file with data summarized by image.
The macro requires confocal images with file_name_CH00, CH01, etc as well as a merge image. The prefix must match between each file name and spaces are not accepted.
- Install Fiji
- Open Fiji and run the python script by selecting to run a macro.
You many not have matching file name formats for channel identification - you must edit the script inside the python file to match your file names.
Written by Rhalena Thomas, Eddie Cai and Harris Nami
If you use this macro in your research please site this github repo. You may also site https://doi.org/10.1093/braincomms/fcab223