HOTARU
High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse
Author
TAKEKAWA Takashi takekawa@tk2lab.org
References
- Takekawa., T, et. al., bioRxiv, https://biorxiv.org/content/10.1101/2022.04.05.487077v2 (2023).
- Takekawa., T, et. al., bioRxiv, https://biorxiv.org/content/10.1101/2022.04.05.487077v1 (2022).
- Takekawa., T, et. al., bioRxiv, https://www.biorxiv.org/content/10.1101/215145 (2017).
Install
Require
- python >=3.10,<3.12
- jax >= 0.4
Recommended
- Nvidia GPU
- cuda 12.0
- cudnn 8.9
Install Procedure (using venv)
- Create venv environment for hotaru
python3.10 -m venv hotaru
- Activate hotaru environment
source hotaru/bin/activate
- Install hotaru
pip install hotaru
Usage
see help
hotaru --help
Demonstration
Download sample.tif
hotaru data.imgs.file=sample.tif mode=test
# see figs/test_*.pdf
hotaru data.imgs.file=sample.tif mode=run
# see figs/run_*.pdf