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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

24 Downloads

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 (2020). Jerman Enhancement Filter (https://github.com/timjerman/JermanEnhancementFilter), GitHub. Retrieved .

Comments and Ratings (18)

heba sal

Xin Zhang

Ayubu Hassan Mbaga

thanks so much, Such useful !

Abir AFFANE

Please can someone explain how to define sigma ??

krishnakumar s

thank you

Mousab Hamd

can we do this in python ?

dekel vered

kangkang jiang

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

Refika Sultan DOGAN

May

Thank you so much. It's really useful.

Hoa Huynh Thai

Thanks a lot, it's very useful

Nghia Nguyen

very good source code

Lennart

Arso

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

Inspired by: Hessian based Frangi Vesselness filter

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