The aim of this macro is to measure the intensity of individual cells in a monolayer using Cellpose to segment the cells in Fiji
To install, drop the file in Fiji.app>macros>toolsets folder. Restart Fiji and the macro name will then appear under the >> menu on the right hand side of Fiji bar.
This macro requires PTBIOP from the Fiji plugins updater. Please follow the instructions from their website to install Cellpose GUI and cite the respective authors.
To activate the macro, find it under the >> menu on the right hand side of Fiji bar. Two buttons should appear on the Fiji bar.
Three buttons will appear, the first one doing the segmentation using Cellpose. It takes as an input a folder with all the CZI files, and gives the rois as output. The macro will ask which channel correspond to the membrane staining, which one is the nuclei staining.
The second button will load back the ROI files and do the rings depending on the thickness entered. So far, it is making a band by shrinking the rois. The program is making the assumptions that all images are the same size within the batch of images.
The third button is just to do the measurement of those rings for all channels. The output will be a csv file containing the results.
Please cite Cellpose if you use this macro.
(0.0.1) Segment using Cellpose for individual cells
(0.1.0) Add Dialog box
(0.1.1) Tasks splitted into three buttons
(0.1.2) Add size filter for cell detections