Biology subjects

Shantanu Singh

Publications and source records attributed to Shantanu Singh.

2 recordsLinked to original sources

bioRxiv2016

CellProfiler Analyst: interactive data exploration, analysis, and classification of large biological image sets

SummaryCellProfiler Analyst allows the exploration and visualization of image-based data, together with the classification of complex biological phenotypes, via an interactive user interface designed for biologists and data scientists. CellProfiler Analyst 2.0, completely rewritten in Python, builds on these features and adds enhanced supervised machine learning capabilities (in Classifier), as well as visualization tools to overview an experiment (Plate Viewer and Image Gallery).\n\nAvailabilityCellProfiler Analyst 2.0 is free and open source, available at http://www.cellprofiler.org/releases and from GitHub (https://github.com/CellProfiler/CellProfiler-Analyst) under the BSD license. It is available as a packaged application for Mac OS X and Microsoft Windows and can be compiled for Linux. We implemented an automatic build process that supports nightly updates and regular release cycles for the software.\n\nContactanne@broadinstitute.org\n\nSupplementary informationSupplementary Text 1: Manual to CellProfiler Analyst; updated versions are available at CellProfiler.org/CPA\n\nSupplementary Data 1: Benchmarking performance of classifiers in CPA 2.0 versus CPA 1.0

Bioinformatics↗

bioRxiv2016

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

In morphological profiling, quantitative data are extracted from microscopy images of cells to identify biologically relevant similarities and differences among samples based on these profiles. This protocol describes the design and execution of experiments using Cell Painting, a morphological profiling assay multiplexing six fluorescent dyes imaged in five channels, to reveal eight broadly relevant cellular components or organelles. Automated image analysis software identifies individual cells and measures ~1,500 morphological features (various measures of size, shape, texture, intensity, etc.) to produce a rich profile suitable for detecting subtle phenotypes. Profiles of cell populations treated with different experimental perturbations can be compared to suit many goals, such as identifying the phenotypic impact of chemical or genetic perturbations, grouping compounds and/or genes into functional pathways, and identifying signatures of disease. Cell culture and image acquisition takes 2 weeks; feature extraction and data analysis take an additional 1-2 weeks.

Systems Biology↗