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.


== MiCA - MiToBo Cell Image Analyzer ==
* [[Applications/CellBoundaryExtractor2D | CellBoundaryExtractor2D]] (since MiToBo 1.8.13.1) <br/> extracts cell boundaries from microscopy images using vesselness enhancement filters.


presented at<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.
''B. Möller and S. Posch,<br/>
'''"MiCA - Easy Cell Image Analysis with Normalized Snakes"'''.<br/>
Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB '11), Heidelberg, Germany, September 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]]'''''
CellImageAnalyzer_2D (since MiToBo version 0.9.6)


'''Main features:'''<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
* Integrated analysis of multi-channel microscope images of cells
* Allows for segmentation of cells, nuclei and sub-cellular structures
* Techniques subsume active contours, wavelets, morphological operators, and others
* Visualization and quantitative summary of segmentation results


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


published in<br/>
* [[Applications/NeuronAnalyzer2D | Neuron Analyzer 2D]]<br/> for segmenting the area of neurites and quantify protein concentrations within these neurites
''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/>
* [[Applications/ScratchAssayAnalyzer | Scratch Assay Analyzer]]<br/> for analysis of collective cell migration based on scratch/ wound closure assay images
Proc. of Iberian Conference on Pattern Recognition and Image Analysis (IbPRIA '11), LNCS 6669, pp. 100-108, Springer, Las Palmas de Gran Canaria, Spain, June 2011.''


'''Name of Plugin:'''<br/>
* [[Applications/CellMigrationAnalyzer | Cell Migration Analyzer]]<br/> for migration analysis based on single cell tracking
ScratchAssay_Analysis (since MiToBo version 0.9.5)
 
'''Description:'''<br/>
* 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
 
 
'''Example images'''<br/>
[http://www.informatik.uni-halle.de/mitobo/downloads/scratch_examples.zip Scratch assay images]
 
== Neuron Analyzer 2D ==
 
The ''Neuron Analyzer 2D'' is available since release version 1.1 of MiToBo. [[File:NeuronAnalyzer2D.png|right|link=]]
 
'''Name of Plugin:'''<br/>
NeuronAnalyzer_2D (since MiToBo version 1.1)
 
'''Main features:'''<br/>
* Neuron boundary detection based on active contours
* Identification of structural neuron parts, like soma, neurites and growth cones
* Morphology analysis, e.g., neurite length, average neurite width, number of branch and end points, growth cone size and shape roundness, etc.
* Extraction of molecular profiles from fluorescently labeld molecules
* Detection of molecular particles, for example FISH data
 
'''Note:''' At the moment this application is only available on Linux OS.
 
'''Example images'''<br/>
...will be available soon

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
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