Code for counting individual cells in colonies

Wondering if there is any available code or macro for counting individual cells in hPSC colonies? There was a method mentioned at ISSCR conference on how to get an accurate single cell count from colonies.


Hi Stefanie,
I apologize for the delay in our response. I believe you are referring to one of our automated methods to count individual hiPSC. Please refer to this bioRxiV version (Automated hiPSC culture and sample preparation for 3D live cell microscopy | bioRxiv) of our recently accepted paper and associated GitHub repo (GitHub - aics-int/celigo_pipeline_automation_paper) that has the pipelines and example data to help you get started on adapting them to your microscope images. Note that some figures have changed in the final version of the paper. We will share the link to this version when it is published. Please let us know if you have additional questions.