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. 2021 Jun 3;11:11793. doi: 10.1038/s41598-021-91191-6

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Development of LabelsToROIs plugin to analyze label images in FIJI/ImageJ. As indicated in (a), the plugin takes as input an original image and a labeled image generated using Cellpose or another software. (b) The plugin allows to automatically extract the segmentations in the label images and generate the corresponding FIJI/ImageJ regions of interest (ROIs). (c) Once generated, the ROIs can be eroded by a fixed number of pixels until the segmentations correctly delineate the objects of interest. The ROI files can be saved, and different measurements can be selected to generate table measurements. (d) The LabelsToROIs plugin also allows for simultaneous processing of multiple images, enabling the generation of ROIs, ROI erosion and table measurements in one step, while automatically saving all the files for future inspection. (e) A diagram of the proposed pipeline for the automatic analysis of skeletal muscle biopsies.