High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse
Project description
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 >=3.11
- jax
Recommended
- Nvidia GPU
- cuda
Install Procedure (using uv)
- Clone git repository
git clone https://github.com/tk2lab/hotaru
- Setup venv
cd hotaru
uv sync
- Activate hotaru environment
source bin/activate
Usage
see help
hotaru --help
Demonstration
Download sample.tif
hotaru data.imgs.file=sample.tif mode=test
# see outputs/{datetime}/test_*.pdf
hotaru data.imgs.file=sample.tif mode=run
# see outputs/{datetime}/run_*.pdf
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