Applications/ScratchAssayAnalyzer: Difference between revisions

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== Scratch Assay Analyzer ==
<br/>
[[File:BF_U2OS_overlay.png|256px|right|link=]]
[[File:GFP_U2OS_overlay.png|256px|right|link=]]
 


== Scratch Assay Analyzer ==
'''Description:'''<br/>
* Quantifies the scratch/ gap areas in monolayer cell culture images (scratch/ gap closure/ wound healing assay)
* Tries to detect already closed scratches via classification utilizing (user trainable) support vector machines (SVM)
* Tested on brightfield, phase contrast and fluorescence images
* Combines the results from images of different time points in a results table


published in<br/>
'''Name of Plugin/Operator:'''<br/>
''M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,<br/>
<code>
'''"Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measures"'''.<br/>
de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
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.''
</code>
<br>
(since MiToBo version 0.9.5)


'''Published in:'''<br/>
''M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,<br/>
''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/>
'''"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.''  
Pattern Recognition, Volume 45, Issue 9, pp. 3154-3165, September 2012.''  


'''Name of Plugin/Operator:'''<br/>
''M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,<br/>
ScratchAssayAnalyzer (since MiToBo version 0.9.5)
'''"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.''
'''Description:'''<br/>
* Quantifies the scratch area in monolayer cell culture images with levelset techniques
* Applicable to brightfield and fluorescence images
* Combines the results from images of different time points in a results table


'''Additional operators contained in the package:'''<br/>
* ScratchAssaySegmenter
** segments single scrach assay images
* ScratchAssaySVMTrainer
** creates or validates SVM models for closed gap detection


'''Example images'''<br/>
'''Example images'''<br/>
[http://www.informatik.uni-halle.de/mitobo/downloads/scratch_examples.zip Scratch assay images]
[http://www.informatik.uni-halle.de/mitobo/downloads/scratch_examples.zip Scratch assay images]

Latest revision as of 13:19, 15 June 2015

Scratch Assay Analyzer

BF U2OS overlay.png
GFP U2OS overlay.png


Description:

  • Quantifies the scratch/ gap areas in monolayer cell culture images (scratch/ gap closure/ wound healing assay)
  • Tries to detect already closed scratches via classification utilizing (user trainable) support vector machines (SVM)
  • Tested on brightfield, phase contrast and fluorescence images
  • Combines the results from images of different time points in a results table

Name of Plugin/Operator:
de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
(since MiToBo version 0.9.5)

Published in:
M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,
"Cell migration analysis: Segmenting scratch assay images with level sets and support vector machines".
Pattern Recognition, Volume 45, Issue 9, pp. 3154-3165, September 2012.

M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,
"Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measures".
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.

Additional operators contained in the package:

  • ScratchAssaySegmenter
    • segments single scrach assay images
  • ScratchAssaySVMTrainer
    • creates or validates SVM models for closed gap detection

Example images
Scratch assay images