Quick StartΒΆ
To get started, install IPFX via pip into a fresh conda evironment. For details see the Installation guide Installation.
Next, example datasets can be downloaded according to the instructions in the Data Access Data Access.
To process a dataset saved in the nwb file, run:
$ python -m ipfx.bin.run_pipeline_from_nwb_file <input_nwb_file> <output_dir>
Input:
- input_nwb_file: a full path to the NWB file with cell ephys recordings
- output_dir: an output directory to save the results
Output:
- input.json: input parameters
- output.json: output including cell features
- output.nwb: NWB file including spike times
- log.txt: run log
- qc_figs: index.html includes cell figures and feature table and sweep.html includes sweep figures