High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse
Project description
HOTARU
High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse
Author
TAKEKAWA Takashi takekawa@tk2lab.org
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 >= 3.8
- tensorflow >= 2.6.1
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
Project details
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hotaru-3.4.1-py3-none-any.whl
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