image analysis

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SOAX is an open source software tool to extract the centerlines, junctions and filament lengths of biopolymer networks in 2D and 3D images. It facilitates quantitative, reproducible and objective analysis of the image data. The underlying method of SOAX uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then stretch along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments.

irene's picture


QuantCenter is the framework for 3DHISTECH image analysis applications. with the goal of helping the pathologists to diagnose in an easier way.

QuantCenter, is optimized for whole slide quantification. It has a linkable algorithm concept that tries to provide an easy-to-use and logical workflow. The user has different quantification modules that he or she could link one after other to fine-tune or to speed up the analysis.

Ofra Golani's picture

Image Processing, Visualization and quantification class by Sam Johnson, Duke University

Image Processing, Visualization and quantification class

Mixture of some lecture-format background information and practical computer exercises using Fiji, slides and example images from 1 day course.

Topics covered in the class include:

Ofra Golani's picture

Image Analysis Course for Life Science by Morten Larsen, University of Copenhagen

Image Analysis Course for Life Science Faculty.
Material includes: slides, hands-on exercises using ImageJ and related data.
There is a full lecture on ImageJ macro language (session 12).
Website: []

Session 1: The basics: Images - Digital image representation, Image processing and image analysis, Concerns at image acquisition, Pixel-wise transformations, Visual enhancement

graemeball's picture


Priism is an image processing, analysis and visualisation application for multidimensional light and electron microscopy data. It uses the Image Visualization Environment (IVE) library, which is a closed-source C library with documented C and FORTRAN APIs. Priism/IVE was developed at UCSF, and can be obtained free of charge by sending an email request to the developers.

volker's picture

Image Processing and Analysis with ImageJ

In this workshop you will learn how to apply image analysis and processing techniques, using the public domain software ImageJ and some additions (plugins and macros). The first part explains the tools available in ImageJ while the second part is centered around image analysis and processing methods. Exercises, solutions and example images are available.

kota's picture


Vaa3D [1, 2, 3] is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions ... It is also Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily...

kota's picture



kota's picture



The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

kota's picture


BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It's a collaborative project, designed and developed by microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and collaborators worldwide. BioImageXD was published in the July 2012 issue of Nature Methods.


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