Metadata-Version: 2.4
Name: roiextractors
Version: 0.6.2
Summary: Python module for extracting optical physiology ROIs and traces for various file types and formats
Author: Heberto Mayorquin, Szonja Weigl, Cody Baker, Alessio Buccino, Paul Adkisson, Alessandra Trapani, Daphné de Quatrebarbes
Author-email: Ben Dichter <ben.dichter@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2020, Ben Dichter Consulting
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Project-URL: Homepage, https://github.com/catalystneuro/roiextractors
Project-URL: Documentation, https://roiextractors.readthedocs.io//
Project-URL: Changelog, https://github.com/catalystneuro/roiextractors/blob/main/CHANGELOG.md
Keywords: ROI,extraction,optical physiology
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
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# ROIExtractors
<p align="center">
  <h3 align="center">Automatically read optical imaging/segmentation data into a common API</h3>
</p>
<p align="center">
   <a href="https://roiextractors.readthedocs.io/"><strong>Explore our documentation »</strong></a>
</p>

<!-- TABLE OF CONTENTS -->

## Table of Contents

- [About](#about)
- [Installation](#installation)
- [Documentation](#documentation)
- [Funding](#funding)
- [License](#license)

## About

ROIExtractors provides a common API for various optical imaging and segmentation formats to streamline conversion and data analysis. ROI stands for Region Of Interest, which is the region in a set of acquired fluorescence images which the segmentation software has determined as a neuron.

Features:

* Reads data from 10+ popular optical imaging and segmentation data formats into a common API.
* Extracts relevant metadata from each format.
* Provides a handy set of methods to analyze data such as `get_roi_locations()`

## Installation

To install the latest stable release of **roiextractors** though PyPI, type:
```shell
pip install roiextractors
```

For more flexibility we recommend installing the latest version directly from GitHub. The following commands create an environment with all the required dependencies and the latest updates:

```shell
git clone https://github.com/catalystneuro/roiextractors
cd roiextractors
conda env create roiextractors_env
conda activate roiextractors_env
pip install -e .
```
Note that this will install the package in [editable mode](https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs).

Finally, if you prefer to avoid `conda` altogether, the following commands provide a clean installation within the current environment:
```shell
pip install git+https://github.com/catalystneuro/roiextractors.git@main
```

## Documentation
See our [ReadTheDocs page](https://roiextractors.readthedocs.io/en/latest/) for full documentation, including a gallery of all supported formats.

## Funding
ROIExtractors is funded by
* Stanford University as part of the Ripple U19 project (U19NS104590).
* LBNL as part of the NWB U24 (U24NS120057).

## License
ROIExtractors is distributed under the BSD3 License. See [LICENSE](https://github.com/catalystneuro/roiextractors/blob/main/LICENSE.txt) for more information.
