Applications: Difference between revisions

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Below you can find selected example applications, some of them have been published already.
Below you can find selected example applications, some of them have been published already.


== MiCA - MiToBo Cell Image Analyzer ==
* [[Applications/PaCeQuant | PaCeQuant]] (released with MiToBo 1.8.6), <br/> for quantifying pavement cell shape in a high-throughput manner


presented at<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
''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/MiCa | MiCA - MiToBo Cell Image Analyzer]]<br/> for segmenting cell boundaries and sub-cellular particles in fluorescent microscopy images
CellImageAnalyzer_2D (since MiToBo version 0.9.6)


'''Main features:'''<br/>
* [[Applications/NeuronAnalyzer2D | Neuron Analyzer 2D]]<br/> for segmenting the area of neurites and quantify protein concentrations within these neurites
* Integrated analysis of multi-channel microscope images of cells
* Allows for segmentation of cells, nuclei and sub-cellular structures
* [[Applications/ScratchAssayAnalyzer | Scratch Assay Analyzer]]<br/> for analysis of collective cell migration based on scratch/ wound closure assay images
* Techniques subsume active contours, wavelets, morphological operators, and others
* Visualization and quantitative summary of segmentation results


== Scratch assay analysis ==
* [[Applications/CellMigrationAnalyzer | Cell Migration Analyzer]]<br/> for migration analysis based on single cell tracking


published in<br/>
* [[Applications/ActinAnalyzer2D | Actin Analyzer 2D]] (since MiToBo 1.4) <br/> for quantifying and comparing actin microfilament structures
''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), LNCS 6669, pp. 100-108, Springer, Las Palmas de Gran Canaria, Spain, June 2011.''
 
'''Name of Plugin:'''<br/>
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 the release of version 1.1 of MiToBo.
 
'''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.
* Optional:
** Extraction of molecular profiles from fluorescently labeld molecules
** Detection of molecular particles, for example FISH data

Revision as of 07:37, 22 September 2017

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

  • PaCeQuant (released with MiToBo 1.8.6),
    for quantifying pavement cell shape in a high-throughput manner
  • 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
  • Actin Analyzer 2D (since MiToBo 1.4)
    for quantifying and comparing actin microfilament structures