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Jerman Enhancement Filter

version 1.0.0.0 (5.69 MB) by Tim Jerman
Enhancement of Vessel/tube and blob/sphere like structures in 2D/3D images using hessian eigenvalues

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Updated 30 May 2017

GitHub view license on GitHub

Available on GitHub.
Jerman's 3D and 2D Hessian based tubular (vessel/vesselness) and spherical (blob/blobness) enhancement filters.
The MATLAB code is the implementation of the next two journal publications:

- T. Jerman, F. Pernus, B. Likar, Z. Spiclin, "Enhancement of Vascular Structures in 3D and 2D Angiographic Images", IEEE Transactions on Medical Imaging, 35(9), p. 2107-2118 (2016), doi={https://doi.org/10.1109/TMI.2016.2550102}

- T. Jerman, F. Pernus, B. Likar, Z. Spiclin, "Blob Enhancement and Visualization for Improved Intracranial Aneurysm Detection", IEEE Transactions on Visualization and Computer Graphics, 22(6), p. 1705-1717 (2016), doi={https://doi.org/10.1109/TVCG.2015.2446493}

and a conference paper (please refer to journal publication [1] for more details):

- T. Jerman, F. Pernus, B. Likar, Z. Spiclin, "Beyond Frangi: an improved multiscale vesselness filter", Proc. SPIE 9413, Medical Imaging 2015: Image Processing, 94132A (2015), doi={https://doi.org/10.1117/12.2081147}

The code is based on Dirk-Jan Kroon's implementation of Frangi's vesselness filter. (www.mathworks.com/matlabcentral/fileexchange/24409-hessian-based-frangi-vesselness-filter)

Tips:

- Make sure that the objects of interest have the highest (if bright compared to the background) or lowest (if dark compared to background) intensities in the image/volume. Scale/normalize the images appropriately.

- The 3D method contains a c-code file that needs to be compiled with "mex eig3volume.c". More info: www.mathworks.com/matlabcentral/fileexchange/24409-hessian-based-frangi-vesselness-filter

- Threshold the filter response to remove any remaining enhanced noise

Content:

- 2D enhancement of vessel/tube-like structures:

- vesselness2D.m - main function
- example_vesselness2D.m - filter applied on a 2D retinal vasculature
- fundus2D.png - image for the example

- 3D enhancement of vessel/tube-like structures:

- vesselness3D.m - main function
- eig3volume.c - fast computation of eigenvalues
- example_vesselness3D.m - filter applied on a 3D cerebral vasculature
- volume.mat - volume for the example

- 3D enhancement of blob/sphere-like structures:

- blobness3D.m - main function
- eig3volume.c - (as above)
- example_blobness3D.m - aneurysm enhancement in a 3D cerebral vasculature
- volume.mat - (as above)

Cite As

Tim Jerman (2019). Jerman Enhancement Filter (https://www.github.com/timjerman/JermanEnhancementFilter), GitHub. Retrieved .

Comments and Ratings (17)

Xin Zhang

thanks so much, Such useful !

Abir AFFANE

Please can someone explain how to define sigma ??

thank you

Mousab Hamd

can we do this in python ?

dekel vered

very good thank you

kang ying

kang ying

I couldn't say love you anymore!!!!!
I spend a lot of time struggling to accomplish the algorithm in your paper.
To be honest, it is a tough work
I can't believe you just put it here
Sincerely, how lucky am I.
Thanks!!!!! I will use it with acknowledgement and citation
Thanks!!!

Laila

huling

May

Thank you so much. It's really useful.

Thanks a lot, it's very useful

very good source code

Lennart

Arso

Updates

1.0.0.0

added acknowledgments

1.0.0.0

added teaser image

MATLAB Release Compatibility
Created with R2015a
Compatible with any release
Platform Compatibility
Windows macOS Linux
Acknowledgements

Inspired by: Hessian based Frangi Vesselness filter