Threshold Variables
Both calcium and voltage imaging pipelines have common threshold variables derived from SciPy’s find_peaks. For more details, refer to the SciPy documentation.
Variable Types:
- min_height - Minimum peak height required.
- min_distance - Minimum horizontal distance (≥1 sample) between peaks. Smaller peaks are removed first until this condition is met.
- min_prominence - Minimum vertical distance a peak must stand out from the baseline, measured between the peak and its lowest contour line.
Determining Prominence
To determine a suitable min_prominence value, test the program with a clear spike trace from a small dataset:
- Select a CZI file with a clear spike trace (can be identified in ImageJ/Fiji by plotting the Z-axis).
- Locate the corresponding TIFF file.
- Place only one or a few TIFF files in a separate folder (the program processes all TIFFs in the given folder).
- Adjust threshold parameters in the pipeline (see the threshold parameter editing section).
- Run the CaImAn GUI program.
- Check the generated CSV files for spike data:
- If zero_spikes.csv is generated for a file that should contain spikes, lower the threshold values and rerun.
CSV Output Files:
| Imaging Type |
Individual File |
Combined File |
| Calcium |
peak_points.csv |
combined_peak_points.csv |
| Voltage |
spike_data.csv |
combined_peak_points.csv |
Spike Determination Insight