https://github.com/openworm/wormsenselab_ash
Electrophysiological recordings of neuron ASH from Wormsense Lab
https://github.com/openworm/wormsenselab_ash
Last synced: about 1 year ago
JSON representation
Electrophysiological recordings of neuron ASH from Wormsense Lab
- Host: GitHub
- URL: https://github.com/openworm/wormsenselab_ash
- Owner: openworm
- Created: 2021-08-26T13:51:28.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2021-09-28T10:25:39.000Z (over 4 years ago)
- Last Synced: 2025-04-13T09:18:45.637Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 19.9 MB
- Stars: 3
- Watchers: 13
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Wormsense Lab Data - ASH
Electrophysiological recordings of [ASH neuron](https://www.wormatlas.org/neurons/Individual%20Neurons/ASHframeset.html) from [Wormsense Lab](https://med.stanford.edu/goodmanlab.html) of Miriam Goodman.
This code uses a metadata spreadsheet and .dat files acquired from the HEKA Patchmaster software to generate NWB files with experimental data.
Example converted data file shown here:
### How to use
The data can be converted by running the following command while in the src directory:
```python
python goodman_to_nwb_conversion.py
```
This `goodman_to_nwb_conversion.py` file can be edited to convert additional datasets, overwrite existing files, or use other metadata spreadsheets (see example below).
```python
metadata_filename = '..//test_data//ASH-metadata_12_III_29.xls'
cell_list = ['ASH097', 'ASH116', 'ASH230', 'ASH287']
overwrite = True
convert_goodman_to_nwb(metadata_filename, cell_list, overwrite)
```
The x_to_nwb module used to convert .dat files to .nwb format was forked from [byte-physics/x_to_nwb](https://github.com/byte-physics/x-to-nwb) and adapted to be compatible with data acquired from older Patchmaster versions (pre v2x90). This module has also been adapted to support a metadata input that can be used to incorporate additional experiment information when generating the NWB file.
### Current state of the project
Note, data is in the process of being moved here from https://github.com/OpenSourceBrain/GSoC_2021_OSB_NWB.
Current outstanding question and remaining to-do items for a fully converted dataset are described in the documentation: [doc/dat_to_nwb_testing.md](doc/dat_to_nwb_testing.md)
### Example datasets
A number of example converted datasets have been added to this repository [here](test_data/README.md).