jb-caliban 0.0.9

Calcium Imaging and Behavior Analysis

caliban: Calcium Imaging and Behavior Analysis

...in dreaming,
The clouds methought would open, and show riches
Ready to drop upon me; that, when I waked,
I cried to dream again.

The Tempest, Act III, Scene ii

Twinkling calcium imaging videos are certainly filled with riches. Whereas Caliban is showered with riches in his slumber, we must dig a little harder to mine these datasets. This software was developed to assist fellow wayward travelers on their journey to understanding how neurons encode information.

This code base was written with the intention of serving as a toolbox for:

1. Statistical Testing of neuron classification by behavior.
2. Visualization of neural activity and behavior data
3. Graph Theoretical Analysis of networks of neurons.
4. Data Visualization tool -- see the "full picture" of the data garnered from experiments with integration of calcium imaging movies, behavioral videos, and data processing results.
5. processing behavior data with Google Colab notebooks

For any feature requests, create an issue.

Getting Started on Google Colab

The package can be run on Google Colab in the following ways

!pip install jb-caliban

for developers:

git clone -b dlc_pypi https://<your_github_token>@github.com/GergelyTuri/caliban.git

%cd caliban

!git pull

!pip install .

Troubleshooting

Create an issue