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


Keywords
Calcium, Imaging, Spike, Detection, Cell, Extraction
License
GPL-3.0-only
Install
pip install hotaru==5.0.1

Documentation

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

Install

Require

  • python >=3.10,<3.12
  • jax >= 0.4
  • 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