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Cytomine

Cytomine is a rich internet application using modern web and distributed technologies (Grails, HTML/CSS/Javascript, RESTful API, Docker), databases (spatial SQL and NoSQL), and machine learning (it currently includes tree-based approaches with random subwindows) to foster active and distributed collaboration and ease large-scale image exploitation.

kota's picture

OpenMOLE

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.

kota's picture

Bio7

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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.

dscho's picture

ImageJ

BioImage Analysis Tool for all! See [1].

ImageJ 1.x http://imagej.net/index.html

ImageJ2 http://imagej.net

dscho's picture

Icy

Reproducing an experiment doesn’t stop at the bench when images are concerned. Icy is an open source bioimaging software package that aims to provide a framework for authors to share, and others to reproduce, research once the sample hits the microscope. Icy was released in April 2011 and is being developed at the Quantitative Image Analysis Unit at the Pasteur Institute in France by Jean-Christophe Olivo-Marin and his team.

dscho's picture

ImgLib2

ImgLib2 is a generic, multi-dimensional data processing library allowing for processing algorithms to be defined in a data-type, dimension, and container independent manner. Due to its interface-based design, it is easy to write adapters to virtually all existing data containers. It is the basis of KNIME, ImageJ2 and a couple of Fiji plugins.

dscho's picture

Fiji

Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences. It is a free, open-source, community-driven project.

Anonymous's picture

OMERO.insight client

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OMERO.server

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