BIF staff offer consultations and comprehensive Image Analysis assistance as needed. With any questions, contact: bif@northwestern.edu
Open Source Software For Your Personal Computer
ImageJ is a Java-based image processing program developed as a collaboration between the National Institutes of Health (NIH) and Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin. ImageJ is the best known and longest-lived open source software for biomedical image analysis.
FIJI (Download, Video Tutorials, Tutorials)
Fiji is a distribution of ImageJ. It is a “ready-to-use” bundle of ImageJ plugins for use in life sciences. The software is primarily targeted at researchers with minimal computer skills, but because ImageJ functionality can be easily extended with plugins, it has also been attractive for researchers with software development skills.
Cell profiler (Download, Tutorials, Manual)
Cell profiler developed by Broad Institute of MIT and Harvard is a MATLAB based free open source software, that enables biologists and scientists to analyze and batch-process cells in biological images. It has a flexible modular design and a user-friendly GUI which allows the user to point and click to do most tasks. The individual modules can be assembled into a pipeline, which later automatically analyzes the images. A typical pipeline consists of loading the images, correcting for uneven illumination, identifying the objects, and then taking measurements on those objects. These modules can easily be added, removed, or rearranged within a pipeline.
QuPath (Download, Video Tutorials, Manual)
Designed by Pete Bankhead at the Queen’s University Belfast QuPath is a comprehensive free open source desktop software application designed specifically to analyze whole slide images. Its primary use is biomarker analysis/ IHC quantification (whole slides and tumor microarrays), but it has also been used for tumor analysis on H&E.
Icy (Download, Video Tutorials, Manual)
Icy, a free open source software founded by Institute Pasteur and France-BioImaging. In Icy users can visualize, annotate and quantify bioimaging data. It is designed as a common platform for image analysis scientists, who can develop new algorithms and life scientists looking for an intuitive tool for image analysis.
Ilastik (Download, Video Tutorials, Manual)
Ilastik is an easy-to-use free open source tool which allows users without expertise in image processing to perform segmentation and classification of 2, 3 and 4D images in a unified way. Through a random forest classifier, ilastik learns from labels provided by the user through a convenient graphical user interface. Based on these labels, ilastik applies a problem specific segmentation.
Orbit (Download, Video Tutorials)
Orbit Image Analysis is a free open source software for quantifying large-format images such as whole slide images of tissue. It can load images from local disk or connect to an Open Microscopy Environment image server (Omero) and can process images on a local computer or on a cluster using Spark job server. Features of the software include many built-in image analysis algorithms for tissue quantification using machine learning techniques, object/cell segmentation, and object classification.