Free Software Tools For Digital Image Analysis


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

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

NIH ImageJ

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.

Color Deconvolution for TMA images using ImageJ

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