/gcamp-analysis

Segmentation and analysis code for GCaMP imaging in PC12 cells

Primary LanguageJupyter NotebookGNU General Public License v3.0GPL-3.0

GCaMP Analysis

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 StarDist
  • gcamp_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.