README.md

HOTARU

High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse

Author

TAKEKAWA Takashi [email protected]

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

Demo Movies