segmentation

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MATLAB

MATLAB is famous, so this page is only for being the landing page for components and workflows.

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Aquiarium

Acquiarium is 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.

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3D Slicer

Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X.

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BioImageXD

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.

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ITK

ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data. It is widely used and contributed in the medical imaging field.

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Schnitzcells

Schnitzcells is a MATLAB based software that allows for quantitative analysis of fluorescent time-lapse movies of living cells. The software package is developed most specifically for bacteria and has been instrumental in analyzing E.coli and B. subtilis movies.
The software contains functions that segment cells (based on either fluorescence or phase images),tracks cells in a frame-to-frame manner,build lineage trees and quantitatively extracts fluorescence.

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Matlab Image Processing Toolbox

The Matlab image processing toolbox extends the Matlab core functionality with general purpose image processing capabilities. This ranges from image access (read / write), common filters (convolution, morphology, order based, Wiener, feature extraction, image enhancement, ...), image transformation (rotation, affine transformation, ...) to segmentation algorithms (thresholding, watershed, region growing). There is also an extensive list of functions to deal with binary or label mask and perform for instance connected particle analysis or morphological operations.

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ilastik

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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Imaris

Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space.

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EBImage

EBImage is an open source image processing and analysis package for the statistical programming language R. Its primary goal is to enable automated analysis of large sets of images such as those obtained in high-throughput screening. An extensive range of basic image processing and feature extraction methods are provided. EBImage is available through the Bioconductor software project (www.bioconductor.org).

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