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
git clone https://github.com/tk2lab/hotaru
- Setup venv
cd hotaru
uv sync
- Activate hotaru environment
source bin/activate
Usage
see help
hotaru --help
Demonstration
Download sample.tif
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
1 maintainer
Release files for hotaru 5.2.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| hotaru-5.2.5.tar.gz | 192.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| hotaru-5.2.5-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 279.2 kB
Release files / hotaru-5.2.5.tar.gz
| Download URL | hotaru-5.2.5.tar.gz |
|---|---|
| Size | 192.0 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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Yes |
| Uploaded via |
uv/0.9.26 {"installer":{"name":"uv","version":"0.9.26","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
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Release files / hotaru-5.2.5-py3-none-any.whl
| Download URL | hotaru-5.2.5-py3-none-any.whl |
|---|---|
| Size | 87.2 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
uv/0.9.26 {"installer":{"name":"uv","version":"0.9.26","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
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