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. 2020 Oct 6;8:558880. doi: 10.3389/fbioe.2020.558880

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Copyright © 2020 Rasse, Hollandi and Horvath.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Cobblestones notebook: Segmentation of non-roundish cells (A,B) Segmentations (red line) of the Cellpose Cyto 0.4 model are superimposed onto the original image subjected to [median 3 × 3] preprocessing. The inverted image (not shown) was used as input to the segmentation. Outlines are well defined, no objects were missed, none over-segmented. These settings fit accurately to the entire dataset (train and test) shown in panels (C,D). Only in one image, three objects were missed and one was over-segmented. Borders around these stones are hard to discern. Individual objects are false color-coded in panels (C,D). The red squares in panel (D) highlight one of the two problematic regions shown as a close-up in panels (E,F).