Python-based segmentation tool for analyzing electrophysiology recordings. It allows to load ABF files, visualize the data, and manually mark segments of interest. The tool provides options to mark segments as bursts or discard and save the segment information in a CSV file.
- clone the repository to your local machine:
git clone https://github.com/ramonitzzz/EphysAnalysis.git
- create virtual environment
conda create ephysAnalysis
conda activate ephysAnalysis
- install required packages
pip install -r ephys_req.txt
- make sure to be in the project directory and to have the virtual environment activated before running the code
python3 SegmentTraces.py
The tool will open a graphical user interface (GUI) window. Use the GUI to navigate through the ABF files, visualize the data, and manually mark segments of interest. Use the buttons in the GUI to mark segments as bursts or discard, save the segment information in a CSV file, or load previously saved segments.
For controling the plot, pressing A) will change the X axis to a 10 second zoom and Y axis to 0 to -500 pA, Z) a 2 second zoom, O) to zoom into a user-defined rectangle, F) for a 180 second by 500 pA zoom, and use + - for finer zooming. Scroll with mouse to advance in the trace, right-click on a segment to edit and double click on a segment to delete.
This project is licensed under the MIT License.