Metadata-Version: 2.1
Name: brainglobe-workflows
Version: 1.0.0
Summary: A collection of end-to-end data analysis workflows executed using BrainGlobe tools.
Author: Christian Niedworok, Charly Rousseau
Author-email: Adam Tyson <code@adamltyson.com>, BrainGlobe developers <code@adamltyson.com>
License: BSD 3-Clause License
        
        Copyright (c) 2023, BrainGlobe developers.
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of the copyright holder nor the names of its
          contributors may be used to endorse or promote products derived from
          this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Project-URL: Bug Tracker, https://github.com/brainglobe/brainglobe-workflows/issues
Project-URL: Documentation, https://brainglobe.info/documentation/brainglobe-workflows
Project-URL: Homepage, https://brainglobe.info
Project-URL: Source Code, https://github.com/brainglobe/brainglobe-workflows
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Image Recognition
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: brainreg >=1.0.0
Requires-Dist: cellfinder-core <1.0.0,>=0.2.4
Requires-Dist: configobj
Requires-Dist: fancylog >=0.0.7
Requires-Dist: imio
Requires-Dist: brainglobe-utils >=0.2.5
Requires-Dist: multiprocessing-logging >=0.3.4
Requires-Dist: natsort
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: packaging
Requires-Dist: pooch
Requires-Dist: scikit-image
Requires-Dist: tifffile
Requires-Dist: tqdm
Provides-Extra: dev
Requires-Dist: black ; extra == 'dev'
Requires-Dist: pytest-cov ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: gitpython ; extra == 'dev'
Requires-Dist: coverage >=5.0.3 ; extra == 'dev'
Requires-Dist: pre-commit ; extra == 'dev'
Requires-Dist: setuptools-scm ; extra == 'dev'
Provides-Extra: napari
Requires-Dist: napari[pyqt5] ; extra == 'napari'
Requires-Dist: brainglobe-napari-io ; extra == 'napari'
Requires-Dist: cellfinder-napari <1.0.0 ; extra == 'napari'

[![Python Version](https://img.shields.io/pypi/pyversions/brainglobe-workflows.svg)](https://pypi.org/project/brainglobe-workflows)
[![PyPI](https://img.shields.io/pypi/v/brainglobe-workflows.svg)](https://pypi.org/project/brainglobe-workflows)
[![Downloads](https://pepy.tech/badge/brainglobe-workflows)](https://pepy.tech/project/brainglobe-workflows)
[![Wheel](https://img.shields.io/pypi/wheel/brainglobe-workflows.svg)](https://pypi.org/project/brainglobe-workflows)
[![Development Status](https://img.shields.io/pypi/status/brainglobe-workflows.svg)](https://github.com/brainglobe/brainglobe-workflows)
[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-workflows/tests)](
    https://github.com/brainglobe/brainglobe-workflows/actions)
[![codecov](https://codecov.io/gh/brainglobe/brainglobe-workflows/branch/master/graph/badge.svg?token=s3MweEFPhl)](https://codecov.io/gh/brainglobe/brainglobe-workflows)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
[![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://brainglobe.info/developers/index.html)
[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info/documentation/brainglobe-workflows/index.html)
[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)

# BrainGlobe Workflows

`brainglobe-workflows` is a package that provides users with a number of out-of-the-box data analysis workflows employed in neuroscience, implemented using BrainGlobe tools.
You can view the [full documentation for each workflow](https://brainglobe.info/documentation/brainglobe-workflows/index.html) online.
You can also find the documentation for the backend BrainGlobe tools these workflows use [on our website](https://brainglobe.info/).

At present, the package offers the following workflows:

- [cellfinder](#cellfinder): Whole-brain detection, registration, and analysis.

## Installation

If you want to install BrainGlobe workflows as a standalone tool, you can run `pip install` in your desired environment:

```bash
pip install brainglobe-workflows
```

`brainglobe-workflows` is built using BrainGlobe tools, and it will automatically fetch the tools that it needs and install them into your environment.
Once BrainGlobe version 1 is available, this package will fetch all BrainGlobe tools and handle their install into your environment, to prevent potential conflicts from partial-installs.

## Contributing

Contributions to BrainGlobe are more than welcome.
Please see the [developers guide](https://brainglobe.info/developers/index.html).

## Citing `brainglobe-workflows`

**If you use any tools in the [brainglobe suite](https://brainglobe.info/documentation/index.html), please [let us know](mailto:code@adamltyson.com?subject=cellfinder), and we'd be happy to promote your paper/talk etc.**

If you find [`cellfinder`](#cellfinder) useful, and use it in your research, please cite the paper outlining the cell detection algorithm:
> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
>
If you use any of the image registration functions in `cellfinder`, please also cite [`brainreg`](https://github.com/brainglobe/brainreg#citing-brainreg).

---

## Cellfinder

Whole-brain cell detection, registration and analysis.

If you want to just use the cell detection part of `cellfinder`, please see the standalone [cellfinder-core](https://github.com/brainglobe/cellfinder-core) package, or the [cellfinder plugin](https://github.com/brainglobe/cellfinder-napari) for [napari](https://napari.org/).

`cellfinder` is a collection of tools developed by [Adam Tyson](https://github.com/adamltyson), [Charly Rousseau](https://github.com/crousseau) and [Christian Niedworok](https://github.com/cniedwor) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).

`cellfinder` is a designed for the analysis of whole-brain imaging data such as [serial-section imaging](https://sainsburywellcomecentre.github.io/OpenSerialSection/) and lightsheet imaging in cleared tissue.
The aim is to provide a single solution for:

- Cell detection (initial cell candidate detection and refinement using  deep learning) (using [cellfinder-core](https://github.com/brainglobe/cellfinder-core)),
- Atlas registration (using [brainreg](https://github.com/brainglobe/brainreg)),
- Analysis of cell positions in a common space.

Basic usage:

```bash
cellfinder -s signal_images -b background_images -o output_dir --metadata metadata
```

Full documentation can be found [here](https://brainglobe.info/documentation/cellfinder/index.html).
