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.


== Neuron Analyzer 2D ==
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* [[Applications/PaCeQuant | PaCeQuant]]<br/> for quantifying pavement cell shape... to appear soon!
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The ''Neuron Analyzer 2D'' is available since release version 1.1 of MiToBo. [[File:NeuronAnalyzer2D.png|right|link=]]
* [[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


'''Name of Plugin/Operator:'''<br/>
* [[Applications/MiCa | MiCA - MiToBo Cell Image Analyzer]]<br/> for segmenting cell boundaries and sub-cellular particles in fluorescent microscopy images
NeuronAnalyzer2D (since MiToBo version 1.1)


'''Main features:'''<br/>
* [[Applications/NeuronAnalyzer2D | Neuron Analyzer 2D]]<br/> for segmenting the area of neurites and quantify protein concentrations within these neurites
* Neuron boundary detection based on active contours
* Identification of structural neuron parts, like soma, neurites and growth cones
* [[Applications/ScratchAssayAnalyzer | Scratch Assay Analyzer]]<br/> for analysis of collective cell migration based on scratch/ wound closure assay images
* 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


'''Installation:'''<br/>
* [[Applications/CellMigrationAnalyzer | Cell Migration Analyzer]]<br/> for migration analysis based on single cell tracking


The R software environment (http://www.r-project.org/) must be installed to use the ''Neuron Analyzer 2D''.<br/>
* [[Applications/ActinAnalyzer2D | Actin Analyzer 2D]] (since MiToBo 1.4) <br/> for quantifying and comparing actin microfilament structures
If R is installed on the system, two environment variables must be set. Perform the following steps on the commandline to set the variables:
 
# export R_HOME="/usr/lib/R" # path to your R installation
# export R_SCRIPTS="/path/to/ImageJ/share/scripts/R" # path to the R scripts, shipped with MiToBo zip file
# libjri.so must be in the LD_LIBRARY_PATH
 
To save these variables permanently, copy the commands above to your local .bashrc file.
 
'''Note:''' The application is currently only available on Linux OS.
 
'''Example images'''<br/>
...will be available soon
 
== Scratch assay analysis ==
 
published in<br/>
''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.''
 
''M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,<br/>
'''"Cell migration analysis: Segmenting scratch assay images with level sets and support vector machines"'''.<br/>
Pattern Recognition, Volume 45, Issue 9, pp. 3154-3165, September 2012.''
 
'''Name of Plugin/Operator:'''<br/>
ScratchAssayAnalyzer (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]
 
== MiCA - MiToBo Cell Image Analyzer ==
 
presented at<br/>
''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/>
CellImageAnalyzer_2D (since MiToBo version 0.9.6)
 
'''Main features:'''<br/>
* 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

Revision as of 15:33, 28 March 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.


  • 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