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+[![DOI](https://zenodo.org/badge/59303623.svg)](https://zenodo.org/badge/latestdoi/59303623)
+
+# Segmentator
+
+<img src="visuals/logo.png" width=420 align="right" />
+
+Segmentator is a free and open-source package for multi-dimensional data exploration and segmentation for 3D images. This application is mainly developed and tested using ultra-high field magnetic resonance imaging (MRI) brain data.
+
+
+The goal is to provide a complementary tool to the already available brain tissue segmentation methods (to the best of our knowledge) in other software packages ([FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), [CBS-Tools](https://www.cbs.mpg.de/institute/software/cbs-tools), [ITK-SNAP](http://www.itksnap.org/pmwiki/pmwiki.php), [Freesurfer](https://surfer.nmr.mgh.harvard.edu/), [SPM](http://www.fil.ion.ucl.ac.uk/spm/software/spm12/), [Brainvoyager](http://www.brainvoyager.com/), etc.).
+
+### Citation:
+- Our paper can be accessed from __[this link.](https://doi.org/10.1371/journal.pone.0198335)__
+- Released versions of this package can be cited by using our __[Zenodo DOI](https://zenodo.org/badge/latestdoi/59303623).__
+
+<img src="visuals/animation_01.gif" width=840 align="center" />
+
+## Core dependencies
+**[Python 3.6](https://www.python.org/downloads/release/python-363/)** or **[Python 2.7](https://www.python.org/download/releases/2.7/)** (compatible with both).
+
+| Package                                        | Tested version |
+|------------------------------------------------|----------------|
+| [matplotlib](http://matplotlib.org/)           | 3.1.1          |
+| [NumPy](http://www.numpy.org/)                 | 1.22.0         |
+| [NiBabel](http://nipy.org/nibabel/)            | 2.5.1          |
+| [SciPy](http://scipy.org/)                     | 1.3.1          |
+| [Compoda](https://github.com/ofgulban/compoda) | 0.3.5          |
+
+## Installation & Quick Start
+- Download [the latest release](https://github.com/ofgulban/segmentator/releases) and unzip it.
+- Change directory in your command line:
+```
+cd /path/to/segmentator
+```
+- Install the requirements by running the following command:
+```
+pip install -r requirements.txt
+```
+- Install Segmentator:
+```
+python setup.py install
+```
+- Simply call segmentator with a nifti file:
+```
+segmentator /path/to/file.nii.gz
+```
+- Or see the help for available options:
+```
+segmentator --help
+```
+
+Check out __[our wiki](https://github.com/ofgulban/segmentator/wiki)__ for further details such as [GUI controls](https://github.com/ofgulban/segmentator/wiki/Controls), [alternative installation methods](https://github.com/ofgulban/segmentator/wiki/Installation) and more...
+
+## Support
+Please use [GitHub issues](https://github.com/ofgulban/segmentator/issues) for questions, bug reports or feature requests.
+
+## License
+Copyright © 2019, [Omer Faruk Gulban](https://github.com/ofgulban) and [Marian Schneider](https://github.com/MSchnei).
+This project is licensed under [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause).
+
+## References
+This application is mainly based on the following work:
+
+* Kniss, J., Kindlmann, G., & Hansen, C. D. (2005). Multidimensional transfer functions for volume rendering. Visualization Handbook, 189–209. <http://doi.org/10.1016/B978-012387582-2/50011-3>
+
+## Acknowledgements
+Since early 2020, development and maintenance of this project is being actively supported by [Brain Innovation](https://www.brainvoyager.com/) as the main developer ([Omer Faruk Gulban](https://github.com/ofgulban)) works there.