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Intravital imaging and 4D quantification of tumor growth and the tumor vasculature

Marta Alabrudzinska, Karolinska Institutet


What are the tools to segment network structures in *3D*?

Try ImarisXT and MATLAB for filling segmented hollow vessels.

What is the desired level of automated analysis vs manual corrections?
What are the properties of 3D skeletons which seems to be relevant for biological problems?
What are the features which can be extracted from current tools?
What are tools which allow to control quality of segmentation?
What are the tools for batching 3D image processing / analysis?
Are there tools to segment 3D cylinders (semantic segmentation)?
What are techniques to segment hollow tubes? Of different diameter?

Ask Bitplane to implement solution
Look at intersection of surface normals (Tischi), defining middle of vessels
Use tools from Graph Theory to analyse extracted network --- e.g. MATLAB’s biograph function
Consider using machine learning (dictionary based) for segmentation (talk also to Daniel Sage)