hotaru 3.3.0

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]

Reference

• Takekawa., T, et. al., Automatic sorting system for large scale calcium imaging data, bioRxiv (2017). https://doi.org/10.1101/215145

Install

Require

• python >= 3.7
• tensorflow >= 2.2.0

Install Procedure (using venv)

• Create venv environment for hotaru
  • python3.x -m venv hotaru
• Activate hotaru environment
  • source hotaru/bin/activate
• Install hotaru
  • pip install hotaru

Usage

Apply Method

• (in hotaru venv)
• mkdir work
• cd work
• cp somewhere/TARGET.tif imgs.tif
• hotaru config
• hotaru run
• (see outs directory)

Config Option

• Set sampling rate of movie
  hotaru config --hz 20.0
• Set mask file (tif or npy)
  hotaru config --mask-type mask.tif
• Set calcium dynamics
  hotaru config --tau-rise 0.08 --tau-fall 0.16
• Set cell size candidate
  hotaru config --radius-type log --radius "2.0,40.0,13"
hotaru config --radius-type linear --radius "2.0,11.0,10"
hotaru config --radius-type manual --radius "2,3,4,5,6,7,8,9,10"

Check Resutls

• (in hotaru venv and in work dir)
• tensorboard --logidr logs
• open in web browser http://localhost:6006