Applications/ScratchAssayAnalyzer: Difference between revisions
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== Scratch Assay Analyzer == | |||
[[File:BF_U2OS_overlay.png|256px|right|link=]] | |||
[[File:GFP_U2OS_overlay.png|256px|right|link=]] | |||
'''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 | |||
'''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.'' | ||
'' | ''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.'' | |||
''' | |||
'''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
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
