Dear BioImage Suite Users,

From an inexperienced Bioimage suite user: I'd like to compare manually delineated contours (created using BioImage Suite's 4D Surface editor applied to a 2D dataset) with those generated by a segmentation algorithm (represented by 2D signed distance functions and stored as .mat files) using the following metrics: mean absolute difference, Hausdorff distance and percentage overlap. If anybody could guide me on which BioImage suite tools that I may be able to use for this, and how I would convert my .mat files into the appropriate format, it would be greatly appreciated.

Best,

N.

You need to be able to export both sets as images in a format that Bioimage Suite can read. The surfaces are easy to do in the surface editor (Use Create Objectmap option), for the matlab stuff you will need to threshold them at 0 and then save them out as nifti .nii files (hopefully with the correct orientation). Once you can do this, there is functionality in BioImage Suite to compute the overlap measures.

XP

Dear Dr. Papademetris,

Thank you for your reply. I just wanted to double-check one point; I know that BioImage Suite can compute the % overlap error - can it also do the MAB and Hausdorff measures?

Thanks again for your help,

Best,

N

The short answer is no unfortunately.

Xenios