CellProfiler 4: Improvements in Speed, Utility and Usability

Stirling, David R.; Swain-Bowden, Madison J.; Lucas, Alice M.; Carpenter, Anne E.; Cimini, Beth A.; Goodman, Allen

doi:10.1101/2021.06.30.450416

Cited by 34 publications

(39 citation statements)

References 18 publications

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“…Images were processed in Zen2 Blue Edition v.2 (Zeiss) and analyzed using CellProfiler v.4.0 (ref. 71 ) with pipelines similar to those previously reported 70 . In brief, the nuclei were identified first and expanded along the intensity gradient of the cytoplasmic staining.…”

Section: Methodssupporting

confidence: 73%

Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells

et al. 2022

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Transplantation of pancreatic islet cells derived from human pluripotent stem cells is a promising treatment for diabetes. Despite progress in the generation of stem-cell-derived islets (SC-islets), no detailed characterization of their functional properties has been conducted. Here, we generated functionally mature SC-islets using an optimized protocol and benchmarked them comprehensively against primary adult islets. Biphasic glucose-stimulated insulin secretion developed during in vitro maturation, associated with cytoarchitectural reorganization and the increasing presence of alpha cells. Electrophysiology, signaling and exocytosis of SC-islets were similar to those of adult islets. Glucose-responsive insulin secretion was achieved despite differences in glycolytic and mitochondrial glucose metabolism. Single-cell transcriptomics of SC-islets in vitro and throughout 6 months of engraftment in mice revealed a continuous maturation trajectory culminating in a transcriptional landscape closely resembling that of primary islets. Our thorough evaluation of SC-islet maturation highlights their advanced degree of functionality and supports their use in further efforts to understand and combat diabetes.

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Section: Methodssupporting

confidence: 73%

Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells

et al. 2022

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“…”, the vast majority of respondents reported the category of “open source point and click software”. The question described such tools to include ImageJ 3 , 4 , Fiji 5 , CellProfiler 6 , Icy 7 , etc., all of which are the most commonly used tools among participants ( Figure 5A ). The next most common tools were “computational libraries and scripts” (such as scikit-image 8 and MATLAB 9 libraries), followed by commercial software on the user’s microscope and other commercial software.…”

Section: Resultsmentioning

confidence: 99%

2020 BioImage Analysis Survey: Community experiences and needs for the future

et al. 2021

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In this paper, we summarize a global survey of 484 participants of the imaging community, conducted in 2020 through the NIH-funded Center for Open Bioimage Analysis (COBA). This 23-question survey covered experience with image analysis, scientific background and demographics, and views and requests from different members of the imaging community. Through open-ended questions, we asked the community to provide feedback for the opensource tool developers and tool user groups. The community's requests for tool developers include general improvement of tool documentation and easy-to-follow tutorials. Respondents encourage tool users to follow the best practice guidelines for imaging and ask their image analysis questions on the Scientific Community Image Forum (forum.image.sc). We analyzed the community's preferred method of learning based on level of computational proficiency and work description. In general, written step-by-step and video tutorials are preferred methods of learning by the community, followed by interactive webinars and office hours with an expert. There is also enthusiasm for a centralized online location for existing educational resources. The survey results will help the community, especially developers, trainers, and organizations like COBA, decide how to structure and prioritize their efforts.

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“…Plates were imaged using a Cytation 5 Cell Imaging Multi-Mode Reader (BioTek) at 20× magnification using the automated imaging function to capture 50 non-overlapping images per well. Background subtraction was performed using Fiji [76] and images were analyzed using CellProfiler v4.2 [77]. A pipeline was generated to identify individual nuclei, trace cell boundaries, segment the cytoplasmic and nuclear compartments, and take measurements of intensity, texture, and correlation with other stains for each type of staining in each subcellular compartment.…”

Section: Methodsmentioning

confidence: 99%

Evidence linking APOBEC3B genesis and evolution of innate immune antagonism by gamma-herpesvirus ribonucleotide reductases

Moraes

Becker

Moghadasi

et al. 2022

Preprint

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Viruses have evolved diverse mechanisms to antagonize host immunity. A recently discovered example is the direct inhibition and relocalization of cellular APOBEC3B (A3B) by the Epstein-Barr virus (EBV) ribonucleotide reductase (RNR) subunit BORF2. Recent reports also indicate interactions between the RNRs of other human herpesviruses and A3B, as well as interactions with the homologous APOBEC3A (A3A) enzyme. Here, we investigate the conservation of this APOBEC3 (A3) counteraction mechanism and reveal novel insights into its evolutionary origin. First, we found that herpesvirus RNRs bind to A3s via partially distinct surfaces. Second, we show that RNR-mediated relocalization and enzymatic inhibition of cellular A3s depend on binding to different regions of the A3 catalytic domain and that the inhibition is specific to A3B. Finally, we show that the ability of viral RNRs to counteract A3s is conserved in herpesviruses that infect humans and Old World monkeys, but absent in viruses infecting New World monkeys that naturally lack A3B. These results combine to indicate that the genesis of A3B at a critical branchpoint in primate evolution may have been a driving force in selecting herpesviruses with an expanded RNR functionality through counteraction of this antiviral enzyme.

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CellProfiler 4: Improvements in Speed, Utility and Usability

Cited by 34 publications

References 18 publications

Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells

Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells

2020 BioImage Analysis Survey: Community experiences and needs for the future

Evidence linking APOBEC3B genesis and evolution of innate immune antagonism by gamma-herpesvirus ribonucleotide reductases

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