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BMC Bioinformatics DOI:10.1186/s12859-021-04344-9

CellProfiler 4: improvements in speed, utility and usability.

Publication TypeJournal Article
Year of Publication2021
AuthorsStirling, DR, Swain-Bowden, MJ, Lucas, AM, Carpenter, AE, Cimini, BA, Goodman, A
JournalBMC Bioinformatics
Date Published2021 Sep 10
KeywordsImage Processing, Computer-Assisted, Microscopy, Software, Workflow

BACKGROUND: Imaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automated and objective analysis of the resulting images is essential to effectively extract biological information from this data. CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements.

RESULTS: Herein we describe CellProfiler 4, a new version of this software with expanded functionality. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimizations to reduce the time and cost associated with running common large-scale analysis pipelines.

CONCLUSIONS: CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to CellProfiler's powerful computational tools in the coming years.


Alternate JournalBMC Bioinformatics
PubMed ID34507520
PubMed Central IDPMC8431850
Grant ListP41 GM135019 / GM / NIGMS NIH HHS / United States
R35 GM122547 / GM / NIGMS NIH HHS / United States
2020-225720 / / silicon valley community foundation /
2018-192059 / / silicon valley community foundation /