Applications: Difference between revisions

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Several image processing pipelines have already been developed in MiToBo. <br/>
Several image processing pipelines have already been developed in MiToBo. <br/>
Below you can find selected example applications, some of them have been published already.
Below you can find selected example applications.


== Scratch assay analysis ==
* [[Applications/CellBoundaryExtractor2D | CellBoundaryExtractor2D]] (since MiToBo 1.8.13.1) <br/> extracts cell boundaries from microscopy images using vesselness enhancement filters.


published in<br/>
* [[Applications/CytoskeletonAnalyzer2D | Cytoskeleton Analyzer 2D]] (since MiToBo 1.8.13) <br/> is an advanced version of the [[Applications/ActinAnalyzer2D | Actin Analyzer 2D]] operator for quantifying and comparing structural patterns of the cytoskeleton in cells, e.g., of actin microfilament structures or microtubuli patterns.
''M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,<br/>
'''"Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measures"'''.<br/>
Proc. of Iberian Conference on Pattern Recognition and Image Analysis (IbPRIA '11), to appear soon, Las Palmas de Gran Canaria, Spain, June 2011.''


'''Name of Plugin:'''<br/>
* [[Applications/PaCeQuantToolset | PaCeQuant]] (released with MiToBo 1.8.6, updated in 2.0), <br/> for quantifying pavement cell shape in a high-throughput manner; the main plugin is supplemented by corresponding tools, i.e. the '''''[[Operators/Tools/Interactive/LabelImageEditor|LabelImageEditor]]''''' and the '''''[[Applications/FeatureColorMapper|FeatureColorMapper]]'''''
ScratchAssay_Analysis (MiToBo version 0.9.5)


'''Description:'''<br/>
* [[Applications/MTBCellCounter | MTB Cell Counter]] (since MiToBo 1.5), <br/> a tool for semi-automatic labeling and counting of spot-like structures like, e.g., plastides, stress granules or p-bodies
* Quantifies the scratch area in monolayer cell culture images with levelset techniques
* Combines the results from images of different time points in a results table


* [[Applications/MiCa | MiCA - MiToBo Cell Image Analyzer]]<br/> for segmenting cell boundaries and sub-cellular particles in fluorescent microscopy images


'''Example images'''<br/>
* [[Applications/NeuronAnalyzer2D | Neuron Analyzer 2D]]<br/> for segmenting the area of neurites and quantify protein concentrations within these neurites
[http://www.informatik.uni-halle.de/mitobo/downloads/scratch_examples.zip Scratch assay images]
* [[Applications/ScratchAssayAnalyzer | Scratch Assay Analyzer]]<br/> for analysis of collective cell migration based on scratch/ wound closure assay images
 
* [[Applications/CellMigrationAnalyzer | Cell Migration Analyzer]]<br/> for migration analysis based on single cell tracking

Latest revision as of 17:59, 16 May 2020

Several image processing pipelines have already been developed in MiToBo.
Below you can find selected example applications.

  • CellBoundaryExtractor2D (since MiToBo 1.8.13.1)
    extracts cell boundaries from microscopy images using vesselness enhancement filters.
  • Cytoskeleton Analyzer 2D (since MiToBo 1.8.13)
    is an advanced version of the Actin Analyzer 2D operator for quantifying and comparing structural patterns of the cytoskeleton in cells, e.g., of actin microfilament structures or microtubuli patterns.
  • PaCeQuant (released with MiToBo 1.8.6, updated in 2.0),
    for quantifying pavement cell shape in a high-throughput manner; the main plugin is supplemented by corresponding tools, i.e. the LabelImageEditor and the FeatureColorMapper
  • MTB Cell Counter (since MiToBo 1.5),
    a tool for semi-automatic labeling and counting of spot-like structures like, e.g., plastides, stress granules or p-bodies
  • Neuron Analyzer 2D
    for segmenting the area of neurites and quantify protein concentrations within these neurites