The algorithm uses image derivatives to segment nuclei in a densely packed 3D tissue. The input file is set of z-slices imaged over time stored in tiff or lsm format ( from Carl Zeiss microscope). After first level of segmentation based on image derivatives, 3D properties are computed. Using these properties image statistics is inferred for the segmented objects and the algorithm implements clustering methods (mind you, computationally time taking!!) to resolve fused nuclei into single ones.
For more details, please read "Object Segmentation and Ground Truth in 3D Embryonic Imaging" published research article (PLOS ONE | DOI:10.1371/journal.pone.0150853). Please refer to this work for citations.
Bhavna Rajasekaran (2020). 3D blob segmentation (https://www.mathworks.com/matlabcentral/fileexchange/67716-3d-blob-segmentation), MATLAB Central File Exchange. Retrieved .
This code only does the 3D nuclei segmentation. The generation of synthetic images is part of the paper, however is not included here.
Hi, I am trying to understand the code but the file log.dat to generate the synthetic images is missing. Could you provide that? Thank you!