hotaru 5.0.1

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

HOTARU

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

Author

TAKEKAWA Takashi [e-mail]

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