CaTrace

A python package for calcium imaging time trace analysis

Usage

See demos/ for how to use the code.
analysis_multi_dataset.ipynb shows how to do multiple dataset analysis.
analysis_OB.py shows how to do single dataset analysis.
tuning_curve_OB.py shows how to do tuning curve clustering.

Structure of the package

• dataio: data reading and writing, contains functions to read data from MATLAB output.
• process_time_trace: preprocess time trace for further analysis.
• manifold_embed: functions for dimensionality reduction.
• pattern_correlation: compute pattern correlation and plotting.
• plot_trace: plotting functions to visualize calcium traces.
• exp_collection: batch processing for multiple datasets.