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BUNPC / psoct_vessel_graphing

Suite of tools for segmenting vessels from PS-OCT images and then converting the segments to a graph.
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Edges incorrectly classified as vessels. #7

Closed mjhyman closed 1 year ago

mjhyman commented 1 year ago

The segmentation script uses a frangi filter to detect cylindrical shapes within the volume, which is a stack of slices. The edges of adjacent slices sometimes have discontinuities that are erroneously classified as segments.

One solution is to take the background subtraction mask, erode (shrink) the borders, and then apply it to the vessel segmentation output. If the mask is eroded by the optimal delta, then it will only remove the erroneously labeled edges.

Another solution may be to use skull stripping on the original PS-OCT volume to blend the discrete slices.

Estimated time to completion : 8 hours

mjhyman commented 1 year ago

The latest push to the branch includes a resolution for this ticket. There are still some edges classified as vessels though. I plan to tune the "mask erosion" to determine the optimal depth for removing all of these false positive vessels.