Metadata-Version: 2.1
Name: big-fish
Version: 0.6.0
Summary: Toolbox for the analysis of smFISH images.
Home-page: https://github.com/fish-quant/big-fish
Author: Arthur Imbert
Author-email: arthur.imbert.pro@gmail.com
License: BSD 3-Clause License
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: Topic :: Scientific/Engineering :: Image Recognition
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: License :: OSI Approved :: BSD License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy (==1.16.0)
Requires-Dist: scikit-learn (==0.21.0)
Requires-Dist: scikit-image (==0.14.2)
Requires-Dist: scipy (==1.4.1)
Requires-Dist: matplotlib (==3.0.2)
Requires-Dist: pandas (==0.24.0)
Requires-Dist: mrc (==0.1.5)
Provides-Extra: deeplearning
Requires-Dist: tensorflow (==2.3.0) ; extra == 'deeplearning'
Requires-Dist: tensorflow-addons (==0.12.1) ; extra == 'deeplearning'

# Big-FISH

[![Build Status](https://travis-ci.com/fish-quant/big-fish.svg?branch=master)](https://travis-ci.com/fish-quant/big-fish)
[![Documentation Status](https://readthedocs.org/projects/big-fish/badge/?version=latest)](https://big-fish.readthedocs.io/en/latest/?badge=latest)
[![codecov](https://codecov.io/gh/fish-quant/big-fish/branch/master/graph/badge.svg)](https://codecov.io/gh/fish-quant/big-fish)
[![License](https://img.shields.io/badge/license-BSD%203--Clause-green)](https://github.com/fish-quant/big-fish/blob/master/LICENSE)
[![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)

**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 |
| ------------- |
| ![](images/plot_cell.png "Nucleus in blue, mRNAs in red, foci in orange and transcription sites in green") |

## 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 (== 0.21.0)
- 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)

Updated dependencies are not tested yet and might break.

### 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.

## 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 unitary tests, run : 

```bash
pytest bigfish
```


