Convert segmentation to closed curve markup

Hi there,
Is there a way I can convert a Segmentation to a Closed Curve Markup by sampling the outside boundary of the segmented area with a certain number of points? I find it significantly faster to use the Draw tool in Segment Editor to outline my specimens than to place hundreds of points with the Closed Curve Markup tool. However, I would like to export my outlines as json files rather than nrrd files, so they are easier to work with in R. Appreciate any suggestions you have.


Do you work with 3D data or just a single 2D image?

For 3D data, planar contour representation is highly problematic - based on our experience with RTSTRUCT DICOM information objects).

What is your end goal? What kind of processing or analysis would you like to do?

Hi Andras,
Thanks for your reply! In this case, I am working with 2D images. My end goal is to make a number of measurements based on each outline, and I already have an R script that makes all these measurements and runs model comparison from coordinates in json files (I am not as comfortable in python). I do not think I can export a segmentation in a file format compatible with my R script, so converting the segmentations to closed curve markups would be the quickest solution to finish the pipeline.

I see, it makes sense then. Some 2D measurements (such as perimeter) are indeed the easiest is to compute from a polyline representation.

To get a polyline representation from a labelmap image representation, you can use vtkDiscreteFlyingEdges2D followed by a vtkContourTriangulator. You can use VTK either in Python (in Slicer) or in R.

Perfect, thanks again!