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

Demo Movies