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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. |
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| [[NeuronAnalyzer2D]]
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| == Neuron Analyzer 2D ==
| | [[Applications/MiCa | MiCA - MiToBo Cell Image Analyzer]]<br/> |
| | | [[Applications/NeuronAnalyzer2D | Neuron Analyzer 2D]]<br/> |
| The ''Neuron Analyzer 2D'' is available since release version 1.1 of MiToBo. [[File:NeuronAnalyzer2D.png|right|link=]]
| | [[Applications/ScratchAssayAnalysis | Scratch assay analysis]]<br/> |
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| '''Name of Plugin/Operator:'''<br/>
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| NeuronAnalyzer2D (since MiToBo version 1.1) | |
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| '''Main features:'''<br/>
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| * Neuron boundary detection based on active contours
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| * Identification of structural neuron parts, like soma, neurites and growth cones
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| * Morphology analysis, e.g., neurite length, average neurite width, number of branch and end points, growth cone size and shape roundness, etc.
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| * Extraction of molecular profiles from fluorescently labeld molecules
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| * Detection of molecular particles, for example FISH data
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| '''Installation:'''<br/>
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| The R software environment (http://www.r-project.org/) must be installed to use the ''Neuron Analyzer 2D''.<br/>
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| If R is installed on the system, two environment variables must be set. Perform the following steps on the commandline to set the variables:
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| # export R_HOME="/usr/lib/R" # path to your R installation
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| # export R_SCRIPTS="/path/to/ImageJ/share/scripts/R" # path to the R scripts, shipped with MiToBo zip file
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| # libjri.so must be in the LD_LIBRARY_PATH
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| To save these variables permanently, copy the commands above to your local .bashrc file.
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| '''Note:''' The application is currently only available on Linux OS.<br/>
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| Current version of ''Neuron Analyzer 2D'' uses R version 3.0.2 (2013-09-25) with rJava_0.9-5 (jri_0.5-5)
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| '''Example images'''<br/>
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| [http://www.informatik.uni-halle.de/mitobo/downloads/neuron_examples.zip Neuron example images] | |
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| == Scratch assay analysis ==
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| published in<br/>
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| ''M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,<br/>
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| '''"Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measures"'''.<br/>
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| 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.''
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| ''M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,<br/>
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| '''"Cell migration analysis: Segmenting scratch assay images with level sets and support vector machines"'''.<br/>
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| Pattern Recognition, Volume 45, Issue 9, pp. 3154-3165, September 2012.''
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| '''Name of Plugin/Operator:'''<br/>
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| ScratchAssayAnalyzer (since MiToBo version 0.9.5)
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| '''Description:'''<br/>
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| * Quantifies the scratch area in monolayer cell culture images with levelset techniques
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| * Combines the results from images of different time points in a results table
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| '''Example images'''<br/>
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| [http://www.informatik.uni-halle.de/mitobo/downloads/scratch_examples.zip Scratch assay images]
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| == MiCA - MiToBo Cell Image Analyzer ==
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| presented at<br/>
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| ''B. Möller and S. Posch,<br/>
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| '''"MiCA - Easy Cell Image Analysis with Normalized Snakes"'''.<br/>
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| Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB '11), Heidelberg, Germany, September 2011.''
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| '''Name of Plugin:'''<br/>
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| CellImageAnalyzer_2D (since MiToBo version 0.9.6)
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| '''Main features:'''<br/>
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| * Integrated analysis of multi-channel microscope images of cells
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| * Allows for segmentation of cells, nuclei and sub-cellular structures
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| * Techniques subsume active contours, wavelets, morphological operators, and others
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| * Visualization and quantitative summary of segmentation results
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