A collection is a software that encapsulate a set of bioimage components and/or workflows.

NucleusJ

Description

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Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

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Amira / Avizo Xtra library

Description

Collection of add-ons (recipes, scripts, demos,…) that will help you improve your day-to-day use of Amira-Avizo and PerGeos Software and make you gain both time and efficiency.
Use the Search field to look for specific keywords related to your domain of interest. The different filters also help you target specific resources.

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Epina Image Lab

Description

Epina ImageLab is a Microsoft Windows-based multisensor imaging tool for processing and analyzing hyperspectral images. It is a modular system consisting of a basic engine, a graphical user interface, a chemometrics toolbox and optional user-supplied modules. It supports the most important spectroscopic imaging techniques, such as UV/Vis, infrared, Raman, THz, optical emission/absorption, and mass spectrometry. On top of that Epina ImageLab enables the user to merge hyperspectral images with maps of physical properties and conventional high-resolution color photos. 

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QuickFit 3

Description

QuickFit 3 is a data evaluation software for FCS Fluorescence Correlation Spectroscopy and imagingFCS (imFCS) measurements, developed in the group B040 (Prof. Jörg Langowski) at the German Cancer Research Center (DKFZ). Actually QuickFit 3 itself is a project manager and all functionality is added as plugins. A set of tested plugins for FCS, imagingFCS and some microscopy-related image processing tasks is supplied together with the software.

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Image registration in Matlab with Image Processing Toolbox

Description

Align two images using intensity correlation, feature matching, or control point mapping

Together, Image Processing Toolbox™ and Computer Vision Toolbox™ offer four image registration solutions: interactive registration with a Registration Estimator app, intensity-based automatic image registration, control point registration, and automated feature matching. 

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Adaptive Pixel Representation

Description

A content-adaptive representation of fluorescence microscopy images called Adaptive Particle Representation (APR), which replaces the regular grid of pixels with particles positioned according to image content. This overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks, since the APR can directly be used in processing without going back to pixels.

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Mathematica

Description

Wolfram Mathematica (usually termed Mathematica) is a modern technical computing system spanning most areas of technical computing — including neural networksmachine learningimage processinggeometrydata sciencevisualizations, and others. The system is used in many technical, scientific, engineering, mathematical, and computing fields.

DragonFly

Description

Dragonfly is a software platform for the intuitive inspection of multi-scale multi-modality image data. Its user-friendly experience translates into powerful quantitative findings with high-impact visuals, driven by nuanced easy-to-learn controls.

For segmentation: It provides an engine fior machine Learning, Watershed and superpixel methods, support histological data .

It offers a 3D viewer, and python scripting capacities .

It is free for reserach use, but not for commercial usage.

DragonFly

WormScan

Description

We have developed WormScan, an automated image acquisition system that allows quantitative analysis of each of these four phenotypes on standard NGM plates seeded with E. coli. This system is very easy to implement and has the capacity to be used in high-throughput analysis.