image processing

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flevet's picture


The Microscopy Image Analysis Tool (MIATool) is a software application designed for the viewing and processing of N-dimensional array of images. At its core is an image viewer which allows the traversal of an N-dimensional array of images. Besides the standard display as pixels of varying intensity values, options are available to view the images as mesh or contour plots. The current version of MIATool supports four different image editing tools which can be used to process the images displayed in the viewer.

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:

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.

Niko Kladt's picture


Image processing library for Python

scikit-image is a collection of algorithms for image processing. It is available free of charge and free of restriction. We pride ourselves on high-quality, peer-reviewed code, written by an active community of volunteers.

kota's picture


OpenCV is released under a BSD license and hence it’s free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 6 million.

kota's picture


OpenMOLE (Open MOdeL Experiment) is a workflow engine designed to leverage the computing power of distributed execution environments for naturally parallel processes. A process is told naturally parallel if the same computation runs many times for a set of different inputs, such as model experiment or data processing… It is free software distributed under the AGPLv3 free software license.

dscho's picture


BioImage Analysis Tool for all! See [1].

ImageJ 1.x


dscho's picture


ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data. It is widely used and contributed in the medical imaging field.


dscho's picture


Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space.


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