This code enables segmentation of images of PC12 cells expressing the calcium sensor GCaMP6f and enables extracting information from them.
A rough walkthrough is provided in:
train_gcamp.ipynb
: Generating a model for segmenting labeled PC12 cells from microscopy images. Based on StarDistgcamp_predict.ipynb
: Use the above trained model predict segmentation for images. This was fine-tuned for eventualy analysis.gcamp_analysis.ipynb
: This combines the above two notebooks with filtering cells based on responsivity to final KCl stimulation into a functional analysis for calcium signaling.
Use gcamp_analysis.py
to run analysis on new data.