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big-fish-0.6.2
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مشاهده بیشترتوضیحات
Toolbox for the analysis of smFISH images.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | big-fish-0.6.2 |
| نام | big-fish |
| نسخه کتابخانه | 0.6.2 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Arthur Imbert |
| ایمیل نویسنده | arthur.imbert.pro@gmail.com |
| آدرس صفحه اصلی | https://github.com/fish-quant/big-fish |
| آدرس اینترنتی | https://pypi.org/project/big-fish/ |
| مجوز | BSD 3-Clause License |
# Big-FISH
[](https://badge.fury.io/py/big-fish)
[](https://travis-ci.com/fish-quant/big-fish)
[](https://big-fish.readthedocs.io/en/latest/?badge=stable)
[](https://codecov.io/gh/fish-quant/big-fish)
[](https://github.com/fish-quant/big-fish/blob/master/LICENSE)
[](https://pypi.python.org/pypi/big-fish/)
**Big-FISH** is a python package for the analysis of smFISH images. It includes various methods to **analyze microscopy images**, such **spot detection** and **segmentation of cells and nuclei**. The package allows the user represent the extract properties of a cell as coordinates (see figure below). The ultimate goal is to simplify **large scale statistical analysis** and quantification.
| Cell image (smFISH channel) and its coordinates representation |
| ------------- |
|  |
## Installation
### Dependencies
Big-FISH requires Python 3.6 or newer. Additionally, it has the following dependencies:
- numpy (>= 1.16.0)
- scipy (>= 1.4.1)
- scikit-learn (>= 0.24.0)
- scikit-image (>= 0.14.2)
- matplotlib (>= 3.0.2)
- pandas (>= 0.24.0)
- mrc (>= 0.1.5)
For segmentation purpose, two additional dependencies can be requested:
- tensorflow (== 2.3.0)
- tensorflow-addons (== 0.12.1)
### Virtual environment
To avoid dependency conflicts, we recommend the the use of a dedicated [virtual](https://docs.python.org/3.6/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) environment. In a terminal run the command:
```bash
conda create -n bigfish_env python=3.6
source activate bigfish_env
```
We recommend two options to then install Big-FISH in your virtual environment.
#### Download the package from PyPi
Use the package manager [pip](https://pip.pypa.io/en/stable/) to install Big-FISH. In a terminal run the command:
```bash
pip install big-fish
```
#### Clone package from Github
Clone the project's [Github repository](https://github.com/fish-quant/big-fish) and install it manually with the following commands:
```bash
git clone git@github.com:fish-quant/big-fish.git
cd big-fish
pip install .
```
## Usage
Big-FISH provides a toolbox for the full analysis pipeline of smFISH images. A complete [documentation](https://big-fish.readthedocs.io/en/stable/) is available online.
This package is part of the [FISH-Quant](https://fish-quant.github.io/) framework and several examples are also available as [Jupyter notebooks](https://github.com/fish-quant/big-fish-examples/tree/master/notebooks).
## Support
If you have any question relative to the repository, please open an [issue](https://github.com/fish-quant/big-fish/issues). You can also contact [Arthur Imbert](mailto:arthur.imbert@mines-paristech.fr) or [Florian Mueller](mailto:muellerf.research@gmail.com).
## Roadmap (suggestion)
Version 1.0.0:
- Complete code coverage.
- Unpin deep learning dependencies
- Add a pretrained pattern recognition model
## Development
### Source code
You can access the latest sources with the commands:
```bash
git clone git@github.com:fish-quant/big-fish.git
cd big-fish
git checkout develop
```
### Contributing
[Pull requests](https://github.com/fish-quant/big-fish/pulls) are welcome. For major changes, please open an [issue](https://github.com/fish-quant/big-fish/issues) first to discuss what you would like to change.
### Testing
Please make sure to update tests as appropriate if you open a pull request. You can install exacts dependencies and specific version of [pytest](https://docs.pytest.org/en/latest/) by running the following command:
```bash
pip install -r requirements_dev.txt
```
To perform unit tests, run :
```bash
pytest bigfish
```
## Citation
If you exploit this package for your work, please cite:
> Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller. FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. bioRxiv (2021) https://doi.org/10.1101/2021.07.20.453024
نیازمندی
| مقدار | نام |
|---|---|
| >=1.16.0 | numpy |
| >=0.24.0 | scikit-learn |
| >=0.14.2 | scikit-image |
| >=1.4.1 | scipy |
| >=3.0.2 | matplotlib |
| >=0.24.0 | pandas |
| >=0.1.5 | mrc |
| ==2.3.0 | tensorflow |
| ==0.12.1 | tensorflow-addons |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl big-fish-0.6.2:
pip install big-fish-0.6.2.whl
نصب پکیج tar.gz big-fish-0.6.2:
pip install big-fish-0.6.2.tar.gz