Vessel distance mapping (VDM), vessel segmentation, and pattern assessment
In our daily life, we associate relevance and closeness. VDM is inspired by this simple idea that vessel close to a region of interest are more relevant. VDM is a versatile tool for image post-processing to understand vessel patterns and their relation to physiology and pathologies. While originally developed for MRI, it is currently applied to other imaging modalities as well such as light sheet microscopy. Below you find an overview of VDM projects with a multitude of application to understand vessel patterns and their impact on physiology and pathologies.
To perform vessel distance mapping, the vasculature needs to be segmented. While an active field of research, segmenting small vessels from high resolution 3D data is challenging (see our vessel segmentation challenge).
Scientific contribution & selected publications
- Using VDM to show that hippocampal arterial supply patterns mediate vascular reserve in CSVD patients
Garcia-Garcia B, Mattern H, Vockert N, Yakupov R, Schreiber F, Spallazzi M, Perosa V, Haghikia A, Speck O, Düzel E, Maass A, Schreiber S. Vessel Distance Mapping: A novel methodology for assessing vascular-induced cognitive resilience. NeuroImage 2023, DOI:10.1016/j.neuroimage.2023.120094 *equal contribution
- Using VDM to assess aging-incuded changes in the micrstructure and its interdependency with the venous vasculature.
Knoll C, Döhler J, Northall A, Schreiber S, Mattern H, Kuehn E. Age-Related Differences in Human Cortical Microstructure Depend on Distance to Nearest Vein Brain Communications 2024, DOI: 10.1093/braincomms/fcae321
- Review on how the (micro)vasculature is impacting ALS disease progression. We discuss markers of how to assess the microvascular integrity with MRI (state of the art and promising new techniques) and how vascular supply patterns could play a role as a resistance or resilience mechanism in ALS.
Schreiber S, Bernal J, Arndt P, Schreiber F, Müller P, Morton L, Braun-Dullaeus RC, Valdés-Hernández MC, Duarte R, Wardlaw JM, Meuth SG, Mietzner G, Vielhaber S, Dunay IR, Dityatev A, Jandke S, Mattern H. *Brain Vascular Health in ALS Is Mediated through Motor Cortex Microvascular Integrity. Cells 2023, DOI:10.3390/cells12060957; *equal contribution
- Deep learning vessel segmentation pipeline with a focus on small cerebral vessels and mitigation of imperfect training data.
Chatterjee S, Prabhu L, Pattadkal M, Bortsova G, Sarasaen C, Dubost F, Mattern H, de Bruijne M, Speck O, Nürnberger A. DS6: Deformation-Aware Semi-Supervised Learning: Application to Small Vessel Segmentation with Noisy Training Data. Journal of Imaging 2022, DOI: 10.3390/jimaging8100259
- An openly available, deep learning-based vessel segmentation tool box.
Xu M, Ribeiro FL, Barth M, Bernier M, Bollmann S, Chatterjee S, Cognolato F, Gulban OF, Itkyal V, Liu S, Mattern H, Polimeni JR, Shaw TB, Speck O, Bollmann S. VesselBoost: A Python Toolbox for Small Blood Vessel Segmentation in Human Magnetic Resonance Angiography Data. Aperture Neuro 2024, DOI: 10.52294/001c.123217
- Showing how hippocampal vascularization patterns affect volume of brain regions beyond the hippocampus in aging.
Vockert N, Perosa V, Ziegler G, Schreiber F, Priester A, Spallazzi M, Garcia-Garcia B, Aruci M, Mattern H, Haghikia A, Düzel E, Schreiber S, Maass A. Hippocampal vascularization patterns exert local and distant effects on brain structure but not vascular pathology in old age. Brain Communications 2021, DOI: 10.1093/braincomms/fcab127
Preprints
- Classifying arterial and venous patterns in the putamen with VDM.
Mattern H, Garcia-Garcia B, Böwe S, Mietzner G, Henneicke S, Speck O, Schreiber S. Vessel distance mapping reveals mesoscopic arterial and venous patterns in the putamen. DOI: 10.5281/zenodo.8098900
- Applying VDM to microscopy images to study inflammation and cognitive dysfunction in a CSVD rat model.
Ulbrich P, Morton L, Briese M, Lämmlin N, Mattern H, Hasanuzzaman Md, Westhues M, Khoshneviszadeh M, Appenzeller S, Gündel D, Toussaint M, Brust P, Kniess T, Oelschlegel A, Goldschmidt J, Meuth S, Heinze HJ, Debska-Vielhaber G, Vielhaber S, Becker A, Dityatev A, Jandke S, Sendtner M, Dunay I, Schreiber S. Vascular and neural transcriptomics reveal stage-dependent pathways to inflammation and cognitive dysfunction in a rat model of hypertension DOI: 10.1101/2023.01.20.524921
Vessel segmentation challenge:
- SMILE-UHURA: Small Vessel Segmentation at MesoscopIc ScaLEfrom Ultra-High ResolUtion 7T Magnetic Resonance Angiograms
- Organizers: Chatterjee S, Mattern H, Dubost F, Schreiber S, Nürnberger A, Speck O;
- Conference: IEEE -ISBI 2023, Cartagena de Indias, Colombia:
- DOI: /10.7303/syn47164761
The challenge results are now available as a preprint