ratiometry_fiji_script
Improved version of the ratiometry script used in [this paper|https://doi.org/10.1073/pnas.1613499114]
The script has now been rewritten in Python for Fiji (Jython) allowing for more up-to-date scripting and call of the different commands.
Simply drag and drop the .py file in Fiji and click on the RUN button at the bottom to start the script. Multiple inputs will then be asked:
- Folder with your images: this is where the images you want to analyze are
- Folder to save results: folder where the result images will be saved
- Extension of the input images: Only files with this extension will be processed
- Channel for segmentation
- Channel alignment: in case your channels aren't aligned, this will use [StackReg|http://bigwww.epfl.ch/thevenaz/stackreg/] with the Affine algorithm
- Dealing with thresholding:
- Fully automatic: Script will try to find the best threshold using the Moments algorithm
- Manual once: User input will be required for the 1st image and be then used for the other images
- Fully manual: User input will be required for each images