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 analysis ==


published in<br/>
'''Description:'''<br/>
''M. Glaß, B. Möller, A. Zirkel, K. Wächter, S. Hüttelmaier and S. Posch,<br/>
* Quantifies the scratch/ gap areas in monolayer cell culture images (scratch/ gap closure/ wound healing assay)
'''"Scratch Assay Analysis with Topology-preserving Level Sets and Texture Measures"'''.<br/>
* Tries to detect already closed scratches via classification utilizing (user trainable) support vector machines (SVM)
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.''
* 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:'''<br/>
<code>
de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
</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