This repository contains the cellProfiler pipeline used by the CircaSCOPE system (CircaSCOPE_CellProfiler_pipeline.cppipe), and the MATLAB code (CircaSCOPE_v02_clean.m) that is used subsequently to analyse the data.
Exemplary input of the CellProfiler pipeline (image sets) can be found here: https://doi.org/10.5281/zenodo.5139326.
Exemplary output of the pipeline, which is the input of the MATLAB script, can be found here: https://doi.org/10.5281/zenodo.4588349.
The CellProfiler pipeline was created on version 3.1.9 The matlab code was created on version R2020b