Icy Spot Tracking

Description

Up to version 2 it was known as the ‘Probabilistic particle tracker’ plugin.

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sumproduct

Description

An implementation of Belief Propagation for factor graphs, also known as the sum-product algorithm

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ROI Measure for Icy

Description

ROI measurement plug-in for Icy.

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acquiarium

Description

Acquiarium is open source software (GPL) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation.

It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.

Acquiarium functionalities diagram

Bioconductor

Description

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.

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Luigi

Description

Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

The purpose of Luigi is to address all the plumbing typically associated with long-running batch processes. You want to chain many tasks, automate them, and failures will happen. These tasks can be anything, but are typically long running things like Hadoop jobs, dumping data to/from databases, running machine learning algorithms, or anything else.

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OpenCV / Image Stiching

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OpenCV / Computational Photography

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OpenCV / CUDA

Description

The OpenCV CUDA module is a set of classes and functions to utilize CUDA computational capabilities. It is implemented using NVIDIA* CUDA* Runtime API and supports only NVIDIA GPUs. The OpenCV CUDA module includes utility functions, low-level vision primitives, and high-level algorithms. The utility functions and low-level primitives provide a powerful infrastructure for developing fast vision algorithms taking advantage of CUDA whereas the high-level functionality includes some state-of-the-art algorithms (such as stereo correspondence, face and people detectors, and others) ready to be used by the application developers.

The CUDA module is designed as a host-level API. This means that if you have pre-compiled OpenCV CUDA binaries, you are not required to have the CUDA Toolkit installed or write any extra code to make use of the CUDA.

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