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aaron's picture


IceImarisConnector is a simple commodity class that eases communication between Bitplane Imaris and MATLAB or python using the Imaris XT interface.

maree's picture


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.

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.

Nico's picture


A commercial image analysis software.
It's interface allows to easily perform measurements and image analysis. Your actions can be recorded and a macro (in a basic script language) can then be created. Almost no knowledge in programming is needed. You can also use python.
A SDK is also available to develop stand alone applications in c++.
Additional modules allow to use specific operations (3D operators...

kota's picture


Python(x,y) is a free scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment.

Many python libraries related to numerical calculation are packaged, so you do not need to search and install them individually.

Included libraries are listed here.

kota's picture


IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

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.

dscho's picture


ilastik (the image learning, analysis, and segmentation toolkit) provides non-experts with a menu of pre-built image analysis workflows. ilastik handles data of up to five dimensions (time, 3D space, and spectral dimension). Its workflows provide an interactive experience to give the user immediate feedback on the quality of the results yielded by her chosen parameters and/or labelings.


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