VesselKnife
One of the issues in medical diagnosis is analysis of angiogram images to identify and determine the course blood vessels. The idea behind VesselKnife development is to create a tool that implements algorithms for angiogram segmentation and for converting raster data into vectorized vessel tree description.
The program includes advanced raster image processing algorithms (including vascularity function computation) and algorithms that enable vectorization of data (determination of center lines, bifurcation locations and diameters). The algorithms in part are results of my original studies, other are from Insight toolkit library. The multiscale vascularity function computation and application of skeletonization were proposed by Grzegorz Dwojakowski and Adam Sankowski (PhD students of the Institute of Electronics).
VesselKnife also includes the original algorithms for visualizing three-dimensional image data, including imaging with transparency. 3D images, resulting from various preprocessing procedures, can be displayed with different colors, superimposed and compared. The implementation of the visualization module directly depends on OpenGL library.
The program is still under development. Below there are binaries of test versions. These may be not fully stable releases and they are not fully tested. Software is provided under GPL3 license. Source codes are available from GitLab repository.
Documents
Publications releted to VesselKnife:
- Szczypiński, P. M. (2023, June). Radius Estimation in Angiograms Using Multiscale Vesselness Function. In International Conference on Computational Science (pp. 230-244). Cham: Springer Nature Switzerland. doi pdf
- Florczyk, S. J., Hotaling, N. A., ... Szczypiński, P. M., ... & Simon Jr, C. G. (2023). Measuring dimensionality of cell‐scaffold contacts of primary human bone marrow stromal cells cultured on electrospun fiber scaffolds. Journal of Biomedical Materials Research Part A, 111(1), 106-117. doi pdf
Manual vesselknife.pdf
3D data the example from the manual bifurkacja.nii.gz
This video tutorial shows the steps of image analysis, starting with image segmentation, going through process of binary image skeletonization and ending with the vector description of vessel tree.
Downloads
The software is provided "as is" without warranties of any kind, express or implied, including but not limited to the warranties of merchantability, suitability for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in contract, tort or otherwise, arising from out of or in connection with the software or the use or other dealings in the Software.
Manual: vesselknife.pdf
How to install: vkinstall.pdf
Lite versions for 64bit Linux, using system shared libraries:
Compiled and tested on Kubuntu 22.04 LTS vesselknife2501lite_amd64.tar.gz
Compiled and tested on Kubuntu 24.04 LTS vesselknife2501lite_for24LTS.tar.gz
Version for 64bit Linux: vesselknife2501_amd64.tar.gz
Statically linked with selected libraries.
Version for 64bit Windows: vesselknife2501_win64.zip
Tested on Windows 10
Sources: vesselknife2501_src.zip