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MCShape

15 May 2009 (Updated 21 Dec 2009)

Code covered by the BSD License

Multiparticle Tracking algorithm for cell motion and morphology

File Information
Description	This is a multiparticle version of the CMorph algorithm previously submitted. The algorithm takes the gradient of the image, and then applies decreasing thresholds and fill operations to attempt to identify objects. One it has found the objects, it attempts to pair them up with objects in the previous frame. It was designed to track cells and microbeads in flow cell assays, so it is designed to be biased to look for a flow direction. The program will output two files: 1. A color-coded .avi with object numbers so it is easy to check the results. 2. A .mat file with the tracking results stored as a structure. The field id's will match the object numbers in the video. I hope this tool will help you in your research. If you use this to help with a publication, please cite the work in your methods section. Either my dissertation or the CMorph conference publication, both are listed in the readme file. I will update the references with the appropriate journal paper as soon as it is in press.
Acknowledgements	The author wishes to acknowledge the following in the creation of this submission: CMorph
Required Products	Image Processing Toolbox
MATLAB release	MATLAB 7.5 (R2007b)
Other requirements	Optional for reading compressed formats not supported by mmreader function: videoIO LIBRARY (Gerald Dalley)
Zip File Content
Other Files	license.txt, MCShape03.m, Partwobeads.m, Readme.txt, Twobeads.avi

Tags for This File
Everyone's Tags	biotech, cell morphology, cell tracking, image processing, pharmaceutical
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Updates
22 May 2009	Minor informational update for the submission- no changes to the code.
20 Dec 2009	Updated the references in the Readme.txt file. This update does not impact the code.
21 Dec 2009	Updated the references in Readme.txt. This update does not affect the code.

Tag Activity for this File
Tag	Applied By	Date/Time
biotech	Brian Schmidt	17 May 2009 19:23:14
pharmaceutical	Brian Schmidt	17 May 2009 19:23:14
image processing	Brian Schmidt	17 May 2009 19:23:14
cell tracking	Brian Schmidt	18 May 2009 11:06:05
cell morphology	Brian Schmidt	18 May 2009 11:06:16

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