This is on behalf of a colleague who is interested in using 3D Slicer to visualize and segment vasculature from mouse brains using two-photon imaging.
Specifically, they are interested in volume rendering of the data and do interactive segmentations and vessel tracing within the rendered volume with the aim of getting a 3D reconstructions of the vasculature and extracting data out of these reconstructions such as vessel diameter, length, tortuosity or straightness, branching order and branching angle etc.
He sent some examples of what they are trying to visualize and segment with Imaris currently. Any pointers would be much appreciated.
What would the interactive segmentation consist of? Is this data suitable for thresholding, or would a more involved vessel segmentation algorithm (such as vmtk) be needed?
They trace the vessels in 3d rendering and then algorithm paints the branches, as I understand. In Imaris they don’t seem to use threshold, possibly due to change in intensities as they go deeper into the tissue.
Ultimate goal is to get metrics from those branches, which I guess vmtk can do. But they first need a semi-automated way of extracting them.
@muratmaga can you provide a small sample? It’s hard to tell from the image you posted how easy the task would be. For example, is the pixel spacing isotropic?