Skip to content
A curated list of awesome cytodata resources
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.gitattributes
code-of-conduct.md
contributing.md
readme.md

readme.md

Awesome Cytodata Awesome

A curated list of awesome cytodata resources.

Contents

Software

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.

Datasets

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

Publications related to image-based profiling having minimum of 50 citations by Google Scholar.

Review

Applications

Software

Assays and data collection

Feature extraction

Feature extraction including image analysis and image quality control.

Data preparation

Data preparation including preprocessing extracted features and dimensionality reduction.

Profiling

Profiling including single-cell data aggregation.

Analysis

Analysis including profile similarity measurement, assay quality assessment and downstream analysis.

Contribute

Contributions welcome! Read the contribution guidelines first.

License

CC0

You can’t perform that action at this time.