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# Segmentator



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).__



## 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.

	a/README.md		b/README.md
1	[![DOI](https://zenodo.org/badge/59303623.svg)](https://zenodo.org/badge/latestdoi/59303623)	1	[![DOI](https://zenodo.org/badge/59303623.svg)](https://zenodo.org/badge/latestdoi/59303623)
2		2
3	# Segmentator	3	# Segmentator
4		4
5	<img src="visuals/logo.png" width=420 align="right" />	5
6
7	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.	6	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.
8		7
9		8
10	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.).	9	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.).
11		10
12	### Citation:	11	### Citation:
13	- Our paper can be accessed from __[this link.](https://doi.org/10.1371/journal.pone.0198335)__	12	- Our paper can be accessed from __[this link.](https://doi.org/10.1371/journal.pone.0198335)__
14	- Released versions of this package can be cited by using our __[Zenodo DOI](https://zenodo.org/badge/latestdoi/59303623).__	13	- Released versions of this package can be cited by using our __[Zenodo DOI](https://zenodo.org/badge/latestdoi/59303623).__
15		14
16	<img src="visuals/animation_01.gif" width=840 align="center" />	15
17
18	## Core dependencies	16	## Core dependencies
19	[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).	17	[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).
20		18
21	\| Package \| Tested version \|	19	\| Package \| Tested version \|
22	\|------------------------------------------------\|----------------\|	20	\|------------------------------------------------\|----------------\|
23	\| [matplotlib](http://matplotlib.org/) \| 3.1.1 \|	21	\| [matplotlib](http://matplotlib.org/) \| 3.1.1 \|
24	\| [NumPy](http://www.numpy.org/) \| 1.22.0 \|	22	\| [NumPy](http://www.numpy.org/) \| 1.22.0 \|
25	\| [NiBabel](http://nipy.org/nibabel/) \| 2.5.1 \|	23	\| [NiBabel](http://nipy.org/nibabel/) \| 2.5.1 \|
26	\| [SciPy](http://scipy.org/) \| 1.3.1 \|	24	\| [SciPy](http://scipy.org/) \| 1.3.1 \|
27	\| [Compoda](https://github.com/ofgulban/compoda) \| 0.3.5 \|	25	\| [Compoda](https://github.com/ofgulban/compoda) \| 0.3.5 \|
28		26
29	## Installation & Quick Start	27	## Installation & Quick Start
30	- Download [the latest release](https://github.com/ofgulban/segmentator/releases) and unzip it.	28	- Download [the latest release](https://github.com/ofgulban/segmentator/releases) and unzip it.
31	- Change directory in your command line:	29	- Change directory in your command line:
32	```	30	```
33	cd /path/to/segmentator	31	cd /path/to/segmentator
34	```	32	```
35	- Install the requirements by running the following command:	33	- Install the requirements by running the following command:
36	```	34	```
37	pip install -r requirements.txt	35	pip install -r requirements.txt
38	```	36	```
39	- Install Segmentator:	37	- Install Segmentator:
40	```	38	```
41	python setup.py install	39	python setup.py install
42	```	40	```
43	- Simply call segmentator with a nifti file:	41	- Simply call segmentator with a nifti file:
44	```	42	```
45	segmentator /path/to/file.nii.gz	43	segmentator /path/to/file.nii.gz
46	```	44	```
47	- Or see the help for available options:	45	- Or see the help for available options:
48	```	46	```
49	segmentator --help	47	segmentator --help
50	```	48	```
51		49
52	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...	50	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...
53		51
54	## Support	52	## Support
55	Please use [GitHub issues](https://github.com/ofgulban/segmentator/issues) for questions, bug reports or feature requests.	53	Please use [GitHub issues](https://github.com/ofgulban/segmentator/issues) for questions, bug reports or feature requests.
56		54
57	## License	55	## License
58	Copyright © 2019, [Omer Faruk Gulban](https://github.com/ofgulban) and [Marian Schneider](https://github.com/MSchnei).	56	Copyright © 2019, [Omer Faruk Gulban](https://github.com/ofgulban) and [Marian Schneider](https://github.com/MSchnei).
59	This project is licensed under [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause).	57	This project is licensed under [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause).
60		58
61	## References	59	## References
62	This application is mainly based on the following work:	60	This application is mainly based on the following work:
63		61
64	* 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>	62	* 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>
65		63
66	## Acknowledgements	64	## Acknowledgements
67	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.	65	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.