NWB conversion scripts and tutorials.
Project description
axel-lab-to-nwb
NWB conversion scripts and tutorials. A collaboration with Axel Lab.
Install
To clone the repository and set up a conda environment, do:
$ git clone https://github.com/ben-dichter-consulting/axel-lab-to-nwb.git
$ conda env create -f axel-lab-to-nwb/make_env.yml
$ source activate convert_to_nwb
Alternatively, to install directly in an existing environment:
$ pip install axel-lab-to-nwb
Use
After activating the correct environment, 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 axel_lab_to_nwb import conversion_function
source_paths = {}
source_paths['processed data'] = {'type': 'file', 'path': PATH_TO_FILE}
source_paths['sparse matrix'] = {'type': 'file', 'path': PATH_TO_FILE}
source_paths['ref image'] = {'type': 'file', 'path': PATH_TO_FILE}
f_nwb = 'fly2.nwb'
metafile = 'metafile.yml'
conversion_function(source_paths=source_paths,
f_nwb=f_nwb,
metafile=metafile,
plot_rois=False)
2. Command line:
Similarly, the conversion function can be called from the command line in terminal:
$ python conversion_module.py [processed_data_file] [sparse_matrix_file] [ref_image_file]
[output_file] [metadata_file]
3. Graphical User Interface:
To use the GUI, just run the auxiliary function nwb_gui.py
from terminal:
$ python nwb_gui.py
4. Tutorial:
At tutorials you can also find Jupyter notebooks with the step-by-step process of conversion.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file axel_lab_to_nwb-0.1.0.tar.gz
.
File metadata
- Download URL: axel_lab_to_nwb-0.1.0.tar.gz
- Upload date:
- Size: 10.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/42.0.2.post20191203 requests-toolbelt/0.9.1 tqdm/4.40.2 CPython/3.7.5
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | b99ba40049b4b88cfc8f66c8465e9a638c18c2768f2e13bd500d5e8a4839080a |
|
MD5 | 1e7e926555a57c3e294046587518f73e |
|
BLAKE2b-256 | a03947805e3d8f41f77661fb7dfe806516c6a4f213e1bcd034a1974bab5255b3 |
File details
Details for the file axel_lab_to_nwb-0.1.0-py3-none-any.whl
.
File metadata
- Download URL: axel_lab_to_nwb-0.1.0-py3-none-any.whl
- Upload date:
- Size: 9.4 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/42.0.2.post20191203 requests-toolbelt/0.9.1 tqdm/4.40.2 CPython/3.7.5
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | f1181d3baebfc877d2b8204a95d94b9dfbcdd5b1543fd113d9a43e5d693ee70b |
|
MD5 | 742e7514bbc6e588f8ca7d51a385196f |
|
BLAKE2b-256 | 12a8495dfc58b9a6d2bed9b1b28c48026ee1abf93ef711184f29c10b59ce59e5 |