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. 2021 Sep 10;22:433. doi: 10.1186/s12859-021-04344-9

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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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — User interface refinements in CellProfiler 4. a The new 3D viewer window with plane controls in the top right. b Contrast and normalization adjustment popup available with any image window. c Interface displayed when the “trace” command is called on a module. Arrow icons on the left represent modules which provide data to or use data from the selected module (dot icon). d Selection widget for choosing multiple images for analysis. Images sourced from disabled or missing modules are highlighted. e “Add modules” pane in search mode, the modules list is filtered based on the text entered into the search box. f The Workspace Viewer module displaying a custom overlay of data from the example pipeline