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David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne Elizabeth Carpenter, Beth A. Cimini, Allen Goodman
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.
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Stirling, D. R., Swain-Bowden, M. J., Lucas, A. M., Carpenter, A. E., Cimini, B. A., & Goodman, A. (2021). CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics, 22(1), 433. https://doi.org/10.1186/s12859-021-04344-9
Stirling, David R., et al. "CellProfiler 4: improvements in speed, utility and usability." BMC Bioinformatics, vol. 22, no. 1, 2021, pp. 433, https://doi.org/10.1186/s12859-021-04344-9.
Stirling, David R., Madison J. Swain-Bowden, Alice M. Lucas, Anne Elizabeth Carpenter, Beth A. Cimini, and Allen Goodman. "CellProfiler 4: improvements in speed, utility and usability." BMC Bioinformatics 22, no. 1 (2021): 433. https://doi.org/10.1186/s12859-021-04344-9.
Stirling D. R., Swain-Bowden M. J., Lucas A. M. [и др.] CellProfiler 4: improvements in speed, utility and usability // BMC Bioinformatics. — 2021. — Vol. 22, № 1. — P. 433. — URL: https://doi.org/10.1186/s12859-021-04344-9
@article{stirling2021cellprofiler,
title = {{CellProfiler 4: improvements in speed, utility and usability}},
author = {David R. Stirling and Madison J. Swain-Bowden and Alice M. Lucas and Anne Elizabeth Carpenter and Beth A. Cimini and Allen Goodman},
journal = {BMC Bioinformatics},
year = {2021},
volume = {22},
number = {1},
pages = {433},
doi = {10.1186/s12859-021-04344-9},
url = {https://doi.org/10.1186/s12859-021-04344-9}
}TY - JOUR AU - Stirling, David R. AU - Swain-Bowden, Madison J. AU - Lucas, Alice M. AU - Carpenter, Anne Elizabeth AU - Cimini, Beth A. AU - Goodman, Allen TI - CellProfiler 4: improvements in speed, utility and usability JO - BMC Bioinformatics VL - 22 IS - 1 SP - 433 PY - 2021 DA - 2021/09/10 DO - 10.1186/s12859-021-04344-9 UR - https://doi.org/10.1186/s12859-021-04344-9 ER -
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