The main objective of this project is to convert existing whole-cell patch clamp recordings in ABF format into the open NWB standard and publish these openly on the DANDI archive. This repository will be used to raise issues, track progress and ensure the process is reproducible.

Setup

To setup the conda environment after cloning this repo:

conda env create -f environment.yml
conda activate nwbephys

We are using a forked and modified version of the x-to-nwb repo. To use the modified version, fork and clone that version of the repo and then install the dev version of the library from the directory:

pip install -e /path/to/x-to-nwb

The updates made to the x-to-nwb package also depend on the ndx-dandi-icephys repo. You can try to install it with

pip install ndx-dandi-icephys

or alternatively clone the repo to your local machine and install the development version:

pip install -e /path/to/ndx-dandi-icephys

Process workflow

The conversion process is iterative since there are data issues with respect to duplicate recording IDs, different recording channels used, different stimulation methods used, incomplete metadata (gain, etc.).