haohuihu / jermanenhancementfilter

Jerman's tubular (vessel) and spherical (blob) enhancement filters

Jerman Enhancement Filter

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:

1. 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={10.1109/TMI.2016.2550102}

2. 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={10.1109/TVCG.2015.2446493}

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

3. 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={10.1117/12.2081147}

The code is based on Dirk-Jan Kroon's implementation of Frangi's vesselness filter. (https://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". (For more info visit: https://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)

2D enhancement of blob/disk-like structures (experimental - not published):

• blobness2D.m - main function
• example_blobness2D.m - enhancement of an aneurysm on a vessel (synthetically generated image)
• blob2D.png - image for the example