CellProfiler 4: improvements in speed, utility and usability.

BMC Bioinformatics
Authors
Keywords
Abstract

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.

Year of Publication
2021
Journal
BMC Bioinformatics
Volume
22
Issue
1
Pages
433
Date Published
2021 Sep 10
ISSN
1471-2105
DOI
10.1186/s12859-021-04344-9
PubMed ID
34507520
PubMed Central ID
PMC8431850
Links
Grant list
P41 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