All of the tools below are useful means of quantifying histochemical or immunohistochemical signals from digitally scanned slides. They are all free to use. The OTS Core does not current provide any assistance with the use of these tools.

Ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.

Cell Profiler is free, open-source software for quantitative analysis of biological images.

ImageJ is a free image processing and analysis program written in Java. It is the mainstay program for image processing with numerous useful macros and plugins to analyze a variety if image features.

This is a collection of ImageJ macros (scripts) for performing color deconvolution and analysis of immunohistochemistry (IHC) staining on tissue microarray (TMA) images