Search Results for "segmentation"

ProStack - a platform for image processing and analysis. It implements various image processing methods as separate modules, that can be joined in a complex image processing scenario by use of a graphical user interface. RPMs are available at https://build.opensuse.org/project/repositories/home:mackoel:compbio

WrapImaJ purposes to be a multi-platform wrapper for different Image Processing systems for: - using the Java programming language. The purpose of WrapImaJ is not to combine an exhaustive collection of all functionalities of different imaging system, but to offer a simple, concise Application Programming Interface (API) - allowing to develop imaging software, the source code of which is independent from the underlying imaging system on which it relies. In it's current form, it...

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.

From Amat et al., Nature Methods, 2014*: "The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of fluorescence microscopes, (2) scalability, by analyzing advanced stages of development with up to 20,000 cells per time point, at 26,000 cells min-1 on a single computer workstation, and (3) ease of use, by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. ...

Wisconsin White Matter Hyperintensity Segmentation [W2MHS] and Quantification Toolbox is an open source MatLab toolbox designed for detecting and quantifying White Matter Hyperintensities (WMH) in Alzheimer’s and aging related neurological disorders. WMHs arise as bright regions on T2- weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden.

This is the prototype version of software for robust detecting and segmentation of cell nuclei in 3D fluorescence labeled microscopy images. First release coming soon...

It is often necessary to assign a series of discrete values to continuosly variable data sequenced by time, position, etc., thereby parsing the data into fewer and larger segments of variable width. The 'segment' utility takes an input data stream as a Hidden Markov Model and applies the Viterbi algorithm to find the most likely segmentation path through the data.

...Wilson, University of Michigan. HMMSeg Wavelet.Java was written by Andrew Hemmaplardh, University of Washington. http://noble.gs.washington.edu/proj/hmmseg/ Unsupervised segmentation of continuous genomic data, Bioinformatics 2007 23:1424-1426 See the above references for a more thorough description of the principles behind wavelet smoothing.

Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.

LiverSegm has been developed with the processing of liver images in mind. This software implements a level set based variational approach that incorporates shape priors and appearance models. It uses ITK Snap as interface.

An R package that performs forward-backward fragment assembling segmentation. Reference: BMC Bioinformatics. 2007 May 3;8:145.

3D medical image platform for visualization and image processing. Segmentation with Levels sets. Surface reconstruction with marching Cubes, texture Mapping and Raycasting,DICOM support. Integration environment for VTK, ITK and vtkInria3D under wxWidgets

This project shows how to integrate NVIDIA CUDA GPU programming API into ITK (Insight Segmentation and Registration Toolkit) library

EDA is Graphical User Interface and Matlab compiled application for filtration of LC-MS or GC-MS, based on probalistic methods. Including peaks and compounds segmentation with various visualizations. This software can be used for metabolomics, proteomics

A plugin package for ImageJ that assists with quantification and characterization of vascular networks. The tool regularizes lighting, segments the vessels, and generates a skeletal description that reflects the biological structures of interest.

MASQOT-GUI is an open-source, platform-independent application for two-channel microarray spot quality control. Included is a set of tools for gridding, segmentation, quantification, multivariate spot quality assessment and data visualization.