ccf-widget

Jupyter ipywidget to interactively explore the Allen Mouse Brain Common Coordinate Framework v3, plot dynamic markers, or cell representations. Couple with the nwb-jupyter-widgets for an understanding of electrophysiology.

Installation

pip install ccfwidget

Usage

In Jupyter:

from ccfwidget import CCFWidget
ccf = CCFWidget()
ccf

Examples on Binder:

• Explore the structure tree
• Use markers to represent neuropixels

Additional examples:

• Add a cell type morphology

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