Digital Quantification of Membrane DAB Immunohistochemical Staining in FFPE Cervical Cancer Tissues Using an Open-Source CellProfiler Pipeline [PDF]
Bio-ProtocolImmunohistochemistry (IHC) is a highly specific and widely used laboratory technique for assessing protein localization and expression in tissue samples. Interpretation of 3,3’ diamino benzidine (DAB)-based IHC is often based on observer-dependent manual
Kripa Krishnakumar +6 more
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Automated Morphological Profiling via Deep Learning-Based Segmentation for High-Throughput Phenotypic Screening [PDF]
Journal of ImagingReproducible morphological profiling, particularly for drug discovery, has become an important tool for compound evaluation. Established workflows such as CellProfiler provide a widely adopted foundation for Cell Painting analysis.
Bendegúz H. Zováthi, Philipp Kainz
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Automated Detection of Binucleated Cell and Micronuclei using CellProfiler 2.0 Software
HAYATI Journal of Biosciences, 2013 Micronucleus assay in human peripheral lymphocytes usually used to assess chromosomal damage. Manual scoring of micronuclei can be time consuming and large numbers of binucleated cells have to be analyzed to obtain statistically relevant data. Automation
Dwi Ramadhani, Sofiati Purnami
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CellProfiler 3.0: Next-generation image processing for biology
PLoS Biology, 2018 CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise ...
Tim Becker +2 more
exaly +3 more sources
A workflow for quantifying cell quiescence in 3D spheroids [PDF]
Biochemistry and Biophysics ReportsQuiescence is a reversible, tightly regulated state in which cells exit the cell cycle while retaining the potential to re-enter proliferation upon an appropriate stimulus.
Maria Rita Assenza +2 more
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An Open-Source Automated Pipeline for Quantitative Morphological Analysis of 3D-Bioprinted Cancer Cell Spheroids [PDF]
Methods and ProtocolsThree-dimensional (3D) culture systems that recapitulate the tumor microenvironment are essential for studying cancer cell behavior, drug response, and cell–matrix interactions.
Pius N. Amartey +3 more
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Protocol for immunofluorescence detection and quantitative analysis of pH-dependent transcriptional condensates [PDF]
STAR ProtocolsSummary: Acidic pH regulates the assembly of transcriptional condensates containing BRD4 and MED1 in a variety of mouse and human cells. Here, we present a protocol to image and quantify BRD4 condensates in bone marrow-derived macrophages.
Zhongyang Wu +4 more
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TrackRefiner a tool for refinement of bacillus cell tracking data [PDF]
npj Systems Biology and ApplicationsSingle-cell resolution time-lapse microscopy of bacterial populations is a powerful tool for assessing cellular behavior and interaction dynamics. Realizing its full potential requires accurate image analysis: segmentation of individual cell objects ...
Atiyeh Ahmadi +3 more
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High-throughput bacterial aggregation analysis in droplets [PDF]
Scientific ReportsMicrofluidic droplet platforms provide a rapid tool to study and capture bacterial aggregation in a well-controlled micro-environment, while image analysis presents an easily available technique to investigate droplet contents.
Merili Saar-Abroi +9 more
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A semi-automated algorithm for image analysis of respiratory organoids. [PDF]
PLoS Computational BiologyRespiratory organoids have emerged as a powerful in vitro model for studying respiratory diseases and drug discovery. However, the high-throughput analysis of organoid images remains a challenge due to the lack of automated and accurate segmentation ...
Anna Demchenko +6 more
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