morphology

Primary tabs

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Blob segmentation

Workflow Language: 
Java
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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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Cell segmentation and measurements

Workflow Language: 
CellProfiler Pipeline
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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.

Strengths

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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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Mahotas

This library gives the numpy-based infrastructure functions for image processing with a focus on bioimage informatics. It provides image filtering and morphological processing as well as feature computation (both image-level features such as Haralick texture features and SURF local features). These can be used with other Python-based libraries for machine learning to build a complete analysis pipeline.

Mahotas is appropriate for users comfortable with programming or builders of end-user tools.

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PINK

Pink is an generic image processing library with inclination towards morphology, discrete topology, skeletonization and image segmentation. Operators support 2D, 3D and 4D images where there exist algorithms for such extensions. There is no practical limitation about the image site. It is suitable for general image processing or as a preprocessing / postprocessing toolset for specific image processing problems.
There are several successfull applications of PINK in the fields of Biology, Material Sciences, Education and Image Processing Research.

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