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. Author manuscript; available in PMC: 2024 Aug 1.
Published in final edited form as: J Pathol. 2023 May 26;260(4):390–401. doi: 10.1002/path.6090

Figure 2. 3D nuclear segmentation pipeline for biopsies imaged with OTLS microscopy.

Figure 2.

(A) Nuclear channel (To-Pro-3) of a PCa biopsy imaged by OTLS microscopy with the cancerous region outlined with a dashed red box. (B) The cancerous region is broken up into discrete data blocks before processing. (C) Each data block is passed into a two-step preprocessing procedure before segmentation (see text for details). (D) Preprocessed data blocks are passed into cellpose to generate 3D nuclear segmentation masks, where each segmented nucleus is assigned a unique label.