# HOTARU
High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse
### Author
TAKEKAWA Takashi <[email protected]>
### 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 >= 3.6.1
- 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`
没有合适的资源?快使用搜索试试~ 我知道了~
资源推荐
资源详情
资源评论
收起资源包目录
hotaru-3.0.1.tar.gz (62个子文件)
hotaru-3.0.1
PKG-INFO 2KB
pyproject.toml 842B
LICENSE 34KB
src
hotaru
train
variance.py 3KB
dynamics.py 2KB
summary.py 2KB
__init__.py 0B
spike.py 2KB
model.py 2KB
footprint.py 2KB
image
mask.py 1010B
filter
gaussian.py 494B
__init__.py 0B
laplace.py 832B
neighbor.py 255B
std.py 947B
__init__.py 0B
max.py 171B
load.py 2KB
cor.py 791B
footprint
find.py 1KB
make.py 2KB
clean_model.py 2KB
clean.py 2KB
util.py 807B
__init__.py 0B
segment.py 2KB
reduce.py 718B
__main__.py 56B
__init__.py 68B
console
application.py 960B
peak.py 1KB
test.py 3KB
clean.py 4KB
run.py 873B
__init__.py 863B
spike.py 1KB
status.py 1KB
footprint.py 1KB
segment.py 3KB
config.py 3KB
output.py 3KB
base.py 3KB
history.py 1KB
data.py 2KB
util
numpy.py 258B
dataset.py 682B
tfrecord.py 490B
pickle.py 269B
__init__.py 0B
gs.py 755B
distribute.py 2KB
csv.py 449B
version.py 86B
optimizer
regularizer.py 1KB
__init__.py 0B
prox_optimizer.py 823B
callback.py 480B
prox_nesterov.py 2KB
input.py 2KB
setup.py 3KB
README.md 1KB
共 62 条
- 1
资源评论
挣扎的蓝藻
- 粉丝: 13w+
- 资源: 15万+
上传资源 快速赚钱
- 我的内容管理 展开
- 我的资源 快来上传第一个资源
- 我的收益 登录查看自己的收益
- 我的积分 登录查看自己的积分
- 我的C币 登录后查看C币余额
- 我的收藏
- 我的下载
- 下载帮助
安全验证
文档复制为VIP权益,开通VIP直接复制
信息提交成功