segment-open -- Segment source distribution

What is Segment?

Segment is a comprehensive software package for medical image analysis, widely used in research.

Segment is developed with cardiovascular MRI (CMR) in mind, but it has also been validated using Cardiac CT and Myocardial Perfusion SPECT. The software package can also be used for a wide range of Radiology and Cardiology applications.

What is the Segment Source Distribution?

The Segment source code is regularly exported from Medviso for free use by the academic research community, through the collaboration between Medviso AB and the Cardiac MR Group at Lund University, Sweden. This forms the basis for segment-open, the Segment Source Distribution, which can be found in this repository.

Note that not all functionality in Segment is present in the Source Distribution, and the Source Distribution is neither FDA-approved nor CE-marked, and may not be used for clinical purposes. Some parts of the code is protected (Matlab p-files).

How do I use Segment?

• Please see the Medviso homepage: manuals and tutorial videos.

It is strongly recommended to use Matlab R2019a.

• Using older versions may produce bugs due to non-existent functionality.
• You can have several Matlab installations on the same computer at the same time.

Matlab toolboxes

Required toolboxes for minimal features (load images and manual segmentation) and for perfusion analysis in Segment:

• Computer Vision Toolbox
• Image Processing Toolbox
• Parallel Computing Toolbox
• Mapping Toolbox
• Statistics and Machine Learning Toolbox

Required toolbox for automatic LV and RV segmentation tools:

• Deep Learning Toolbox

Required toolbox for Relaxometry analysis:

• Optimization Toolbox

Required toolbox for AVPD analysis:

• Curve Fitting Toolbox

Required toolbox for LA segmentation:

• Curve Fitting Toolbox

Required toolboxes for SPECT analysis:

• Optimization Toolbox
• Signal Processing Toolbox

Contributions

We'd love to include your plugins in this repository! Please see the Contributions Document for details, as well as the License and Terms of use below.

Found a bug? Do you have a feature request? Please let us know by opening an issue in the tracker!

License and Terms of use

We recommend that you read the full license agreement before starting to use Segment. This section is just a short summary.

Segment is freely available for academic research in source and binary form, provided that you cite relevant publications and the usage of the software in your publications (see specific papers below).

The Segment Source Distribution may not be used for commercial or clinical applications. The commercial, FDA-approved and CE-marked version of Segment is developed, marketed and sold by Medviso AB, Lund, Sweden.

We are happy to accept contributions to this source tree if you want to share your work with the world. Write your code as a Segment plugin and submit your work as a pull request when you feel ready. Please see the Contributions Document for details.

What IS allowed?

Provided that you give proper attribution (see "Papers to cite" below), you can:

• Use Segment for academic research
• Publish results based on Segment
• Write your own plugins
• Share your plugins with others using the Segment source distribution

What IS NOT allowed?

• Clinical use
• Commercial use
• Distributing your own compiled version of Segment
• For any of these cases, please contact Helen Fransson (CEO, Medviso AB, see contact info below)

Papers to cite

According to the license agreement, proper citation of required when you publish research based on Segment. A complete list is kept at the Medviso homepage: http://medviso.com/research/how-to-refer/

Frequently asked questions

Q: What is the airspeed velocity of an unladen swallow?

A: African or European?

Contact