https://github.com/neurodatawithoutborders/ccf-widget
https://github.com/neurodatawithoutborders/ccf-widget
Last synced: 6 months ago
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- Host: GitHub
- URL: https://github.com/neurodatawithoutborders/ccf-widget
- Owner: NeurodataWithoutBorders
- License: mit
- Created: 2020-06-12T18:20:43.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2022-11-21T17:47:51.000Z (over 3 years ago)
- Last Synced: 2024-11-18T15:11:34.446Z (over 1 year ago)
- Language: Python
- Size: 1.82 MB
- Stars: 5
- Watchers: 12
- Forks: 3
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# ccf-widget
Jupyter [ipywidget](https://ipywidgets.readthedocs.io/en/stable/) to
interactively explore the [Allen Mouse Brain Common Coordinate Framework
v3](https://doi.org/10.1016/j.cell.2020.04.007), plot dynamic markers, or cell
representations. Couple with the
[nwb-jupyter-widgets](https://github.com/NeurodataWithoutBorders/nwb-jupyter-widgets)
for an understanding of electrophysiology.
[](https://mybinder.org/v2/gh/NeurodataWithoutBorders/ccf-widget/master?filepath=examples%2FStructureTreeNavigation.ipynb)
## Installation
```shell
pip install ccfwidget
```
## Usage
In Jupyter:
```python
from ccfwidget import CCFWidget
ccf = CCFWidget()
ccf
```
Examples on Binder:
- [Explore the structure tree](https://mybinder.org/v2/gh/NeurodataWithoutBorders/ccf-widget/master?filepath=examples%2FStructureTreeNavigation.ipynb)
- [Use markers to represent neuropixels](https://mybinder.org/v2/gh/NeurodataWithoutBorders/ccf-widget/master?filepath=examples%2FNeuropixelProbes.ipynb)
Additional examples:
- [Add a cell type morphology](./examples/CellTypes.ipynb)
## Troubleshooting
With the error:
```
[...]
IOPub message rate exceeded.
[...]
```
Start `jupyter` with the flag:
```
jupyter notebook --NotebookApp.iopub_msg_rate_limit=1e12
```
## Hacking
Contributions are welcome and appreciated.
To install an editable build:
```
python3 -m pip install flit
flit install --symlink
```