Buffalo-lab-data-to-nwb

Scripts which convert Buffalo lab data to NWB format. Currently we only support conversion for processed data.

authors: Luiz Tauffer, Maija Honig, Ryan Ly, Ben Dichter

Install

pip install git+https://github.com/ben-dichter-consulting/buffalo-lab-data-to-nwb.git

Use

The conversion function can be used in different forms:

1. Imported and run from a python script:
Here's an example: we'll grab the data from the same experiment but stored in different .npz files and save it to a single .nwb file.

from buffalonwb.conversion_module import conversion_function

source_paths = dict()
source_paths['raw Nlx'] = {'type': 'dir', 'path': PATH_TO_DIR}
source_paths['processed Nlx'] = {'type': 'dir', 'path': PATH_TO_DIR}
source_paths['processed behavior'] = {'type': 'file', 'path': PATH_TO_FILE}
source_paths['sorted spikes'] = {'type': 'file', 'path': PATH_TO_FILE}

f_nwb = 'buffalo.nwb'
metafile = 'metafile.yml'

conversion_function(source_paths=source_paths,
                    f_nwb=f_nwb,
                    metafile=metafile,
                    skip_raw=True,
                    skip_processed=False,
                    lfp_iterator_flag=True,
                    no_copy=True)

2. Command line:
Similarly, the conversion function can be called from the command line in terminal:

$ python conversion_module.py [raw_nlx_dir] [lfp_mat_dir]
  [sorted_spikes_nex5_file] [behavior_file] [output_file] [metadata_file]
  [-skipraw] [-skipprocessed] [-lfpiterator] [-dontcopy]

IMPORTANT:
[raw_nlx_dir] and [lfp_mat_dir] should be paths to directories
[sorted_spikes_nex5_file] [behavior_file] [output_file] [metadata_file] should be paths to files

optional inputs add these after the positional arguments to use additional options
"-skipraw" (will skip adding raw data to nwb file)
"-skipprocessed" (will skip adding processed data to nwb file)
"-lfpiterator" (change lfp data method to dataChunkIterator (for large data))
"-dontcopy" (ignore broken copy method by going straight to output file)

3. Graphical User Interface:
To use the GUI, just run the auxiliary function nwb_gui.py from terminal:

$ python nwb_gui.py