>>> This set of Matlab files comprises a cell detector. The only file the user has to launch is ‘analyzeImages.m’. The rest are functions that the script calls during the run. Launch the script and pick the ‘DemoForCellDetector.czi’ file. Then, select the region in which you want to detect the cells. In the end, check out the new .tif file that Matlab has created: it has got the original images with extra labels: green cells co-occuring ALSO in the red channel are circled red, green cells NOT occurring in the red channel are circled blue.

>>> This script will work if you have the Matlab Bioformats library downloaded. Only Bioformats 5.5.2 and lower function properly with this script, higher versions have compatibility issues with the .czi file. More info and download links: https://docs.openmicroscopy.org/bio-formats/5.7.2/users/matlab/index.html#installation

>>> The sensitivity parameters are pre-defined in the ‘parameters.mat’ file. Those are the width of the Fourier 2D filter, the radius of the filter for morphological opening, and the threshold for segmentation. To make sure that these parameters are independent of image brightness, before all analyses, the image is changed so that its brightness histogram will match ’targetHistogram’, the fourth variable in the ‘parameters.mat’ file.

>>> If the user to use custom parameters instead of the ones I predefined, s/he can use ‘GetParameters.mlapp’. This is a GUI for finding the most optimal parameters. Once the optimal parameters have been set on the sliders in the app, all the user has to do is to close the window: parameters will be automatically saved in the updated ’parameters.mat’ file.