A curated list of awesome cytodata resources.
Open source software packages for image-based profiling of biological phenotypes.
- Advanced Cell Classifier Advanced Cell Classifier is a data analyzer program to evaluate cell-based high-content screens and tissue section images.
- CellProfiler CellProfiler is a free open-source software for measuring and analyzing cell images.
- CellProfiler Analyst Interactive data exploration, analysis, and classification of large biological image sets.
- Cytominer Methods for image-based cell profiling.
- EBImage Image processing toolbox for R.
- HTSvis A web app for exploratory data analysis and visualization of arrayed high-throughput screens.
Annotated datasets for image-based profiling.
- Broad Bioimage Benchmark Collection The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely downloadable microscopy image sets. In addition to the images themselves, each set includes a description of the biological application and some type of "ground truth" (expected results).
Publications related to image-based profiling having minimum of 50 citations by Google Scholar.
- Data-analysis strategies for image-based cell profiling Introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images.
- High-content screening for quantitative cell biology Describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions.
- Microscopy-based high-content screening Describe the state of the art for image-based screening experiments and delineate experimental approaches and image-analysis approaches as well as discussing challenges and future directions, including leveraging CRISPR/Cas9-mediated genome engineering.
- Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes This study provides an in-depth analysis of cell division phenotypes and makes the entire high-content data set available as a resource to the community.
- CellProfiler: image analysis software for identifying and quantifying cell phenotypes Describe the first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler.
- CellProfiler Analyst: data exploration and analysis software for complex image-based screens Describe an open-source software package called "CellProfiler Analyst".
- Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software describe CellProfiler 2.0, which has been engineered to meet the needs of its growing user base. It is more robust and user friendly, with new algorithms and features to facilitate high-throughput work.
Assays and data collection
- Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes Protocol describing the design and execution of experiments using Cell Painting.
- Multiplex Cytological Profiling Assay to Measure Diverse Cellular States Cell Painting assay.
Feature extraction including image analysis and image quality control.
- Retrospective shading correction based entropy minimization Method for retrospective shading correction based on entropy minimization.
Data preparation including preprocessing extracted features and dimensionality reduction.
- Minimum redundancy feature selection from microarray gene expression data Minimum redundancy - maximum relevance feature selection framework.
Profiling including single-cell data aggregation.
Analysis including profile similarity measurement, assay quality assessment and downstream analysis.
- Image-based multivariate profiling of drug responses from single cells a multivariate method for classifying untreated and treated human cancer cells based on ∼300 single-cell phenotypic measurements.
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