Metadata-Version: 2.4
Name: hotaru
Version: 5.2.5
Summary: High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse
Author-email: TAKEKAWA Takashi <takekawa@tk2lab.org>
License-Expression: GPL-3.0-only
License-File: LICENSE
Keywords: Calcium Imaging,Cell Extraction,Spike Detection
Requires-Python: >=3.11
Requires-Dist: av>=10.0
Requires-Dist: hydra-core>=1.3
Requires-Dist: jax<0.7,>=0.4.34; sys_platform == 'darwin'
Requires-Dist: jax[cuda12]<0.7,>=0.4.34; sys_platform == 'linux'
Requires-Dist: kaleido>=0.2.1
Requires-Dist: matplotlib>=3.7.2
Requires-Dist: pandas>=2.0.3
Requires-Dist: plotly>=5.0.0
Requires-Dist: psutil>=7.1.0
Requires-Dist: tensorflow>=2.13.0
Requires-Dist: tifffile>=2022.8
Requires-Dist: tqdm>=4.64
Requires-Dist: versioningit
Description-Content-Type: text/markdown

# 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
- 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 >=3.11
- jax

### Recommended
- Nvidia GPU
- cuda

### Install Procedure (using uv)
- Clone git repository
```shell
git clone https://github.com/tk2lab/hotaru
```
- Setup venv
```shell
cd hotaru
uv sync
```
- Activate hotaru environment
```shell
source bin/activate
```

## Usage
see help
```shell
hotaru --help
```

## Demonstration
Download [sample.tif](https://drive.google.com/file/d/12pRyoWFRu-h15BaAAscLyoziAjiY5nP6/view?usp=drive_link)
```shell
hotaru data.imgs.file=sample.tif mode=test
# see outputs/{datetime}/test_*.pdf
hotaru data.imgs.file=sample.tif mode=run
# see outputs/{datetime}/run_*.pdf
```

[Demo Movies](https://drive.google.com/drive/folders/1yZK8vU1WOyCMuU-ogiSB7FJcZUxU8QtP?usp=sharing)
