List of important functions provided in the code base
| Name | Description | Command line | Location | Language |
|---|---|---|---|---|
| synthesis Demo.m | Command line demo, output to file: “synthData-demo.mat”. Generates a synthetic 2-P time cell dataset file | $ cd TimeCellAnalysis/rho-matlab/demos && matlab -nodisplay -nosplash -r “synthesisDemo; quit” | rho-matlab/demos | MATLAB |
| ti_demo.py | Command-line demo, output to console. | $ python TcPy/ti_demo.py sampleData/sample_synth_data.mat | TcPy | Python interface and C++ numerics |
| r2b_demo.py | Command-line demo, output to console. Runs Ridge-to-Background analysis from Modi et al. (2014). Reports R2B Mean and R2B Bootstrap classifications | $ python TcPy/r2b_demo.py sampleData/sample_synth_data.mat | TcPy | Python interface and C++ numerics |
| peq_demo.py | Command-line demo, output to console. Runs parametric equation analysis from current study. Reports PEQ threshold classification, and estimates for noise, event width, imprecision, and hit trial ratio for dataset | $ python TcPy/peq_demo.py sampleData/sample_synth_data.mat | TcPy | Python interface and C++ numerics |
| ground_truth_check.py | Command-line demo, output to console. Uses synthetic data files to assess accuracy of classification by the various Mau and Modi algorithms | $ python TcPy/ground-truth_check.py sampleData/sample_synth_data.mat | TcPy | Python interface and C++ numerics |
| Benchmark.py | Command-line demo, output to console. Simple time and memory benchmarks for the Mau, Modi, or PEQ algorithms | $ python TcPy/run_batch_analysis.py sampleData/sample_synth_data.mat | TcPy | Python interface and C++ numerics |
| run_batch_analysis.py | Command-line production script, output to CSV files. Runs a batch analysis using all methods on a data file. Generates .csv filesfor TI, R2B, PEQ, and ground truth classifications | $ python TcPy/ti_demo.py sampleData/sample_synth_data.mat | TcPy | Python interface and C++ numerics |
| pyBindMap.py | Provides an interface for MATLAB programmers, to the python/C__ fuynctions using two wrapper functions: runTIanalysis and runR2Banalysis | Utility function, not run from command line | TcPy | Python |
| dodFbF.m | Utility function to convert experimental raw 2p calcium activity data from Suite2P to df/F form. | Utility function, not run from command line | rho-matlab/CustomFunctions | MATLAB |
All these functions should be run from the cloned repository, TimeCellAnalysis.