Quantitative Analysis of Dynamic Association in Live Biological Fluorescent Samples
17.04.2014
Quantitative Analysis of Dynamic Association in Live Biological Fluorescent Samples, Pekka Ruusuvuori, Lassi Paavolainen, Kalle Rutanen, Anita Mäki, Heikki Huttunen, Varpu Marjomäki, PLoS ONE 9 (4), 2014.
Abstract
Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed.
Supplementary results
The effect of matching distance parameter on the matching accuracy:
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Data
Here is the data that were used for the experiments:
- Simulation data for low-association experiments (205 MB)
- Simulation data for intermediate-association experiments (205 MB)
- Simulation data for high-association experiments (205 MB)
- Data for real microscope-image experiments (4 MB). These are the segmentation masks from the microscope-image experiments, both fixed and live.
Software
Here is the software that were used to compute the results:
- Pastel was used to perform the point-pattern matching algorithm described in the paper.
- BioImageXD was used for detecting spots and calculating traditional colocalization measures in simulated and real microscopy experiments.
- This Matlab module was used for detecting spots in fluorescence microscope images for alternative spot detection methods.
Links
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Computational Systems Biology Research Group at the Department of Signal Processing, Tampere University of Technology.
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Virus Entry and Regulation of Membrane Traffic at the Nanoscience Center / Department of Biological and Environmental Science, University of Jyväskylä.
Contact
Pekka Ruusuvuori
firstname.lastname@tut.fi
Tampere University of Technology
Pori, P.O. Box 300
FI-28101 Pori, FINLAND