Particle Analysis, Filtering, Colocalization, Deconvolution, Segmentation
The MosaicSuite is a fully integrated suite of various plugins from the MOSAIC Group. It contains tools for 2D and 3D feature point-tracking, 2D and 3D image segmentation, colocalization analysis, interaction analysis, background subtraction, Point-Spread Function (PSF) estimation from images, and simulation of the image-formation process in fluorescence microscopes. The best way to install it is via the MOSAIC Fiji Update site, as described on the MOSAIC web page. The MOSAICsuite interconnects all the different methods from the MOSAIC Group to a coherent workflow package and also contains wizards to assist parameter tuning, as well as support for parallel processing on computer clusters.
I. F. Sbalzarini and P. Koumoutsakos. Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology, Journal of Structural Biology 151(2):182-195, 2005.
J. A. Helmuth, C. J. Burckhardt, U. F. Greber, and I. F. Sbalzarini. Shape reconstruction of subcellular structures from live cell fluorescence microscopy images. Journal of Structural Biology, 167:1–10, 2009.
J. A. Helmuth, G. Paul, and I. F. Sbalzarini. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11:372, 2010.
J. Cardinale, G. Paul, and I. F. Sbalzarini. Discrete region competition for unknown numbers of connected regions. IEEE Trans. Image Process., 21(8):3531–3545, 2012.
A. Shivanandan, A. Radenovic, and I. F. Sbalzarini. MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis. BMC Bioinformatics, 14:349, 2013.
G. Paul, J. Cardinale, and I. F. Sbalzarini. Coupling image restoration and segmentation: A generalized linear model/Bregman perspective. Int. J. Comput. Vis., 104(1):69–93, 2013.
A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I. F. Sbalzarini. Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature Protocols, 9(3):586–596, 2014.
N. Chenouard, I. Smal, F. de Chaumont, M. Maska, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. G. Magnusson, J. Jalden, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J.-Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H.-W. Dan, Y.-S. Tsai, C. O. de Solorzano, J.-C. Olivo-Marin, and E. Meijering. Objective comparison of particle tracking methods. Nature Methods, 11(3):281–289, 2014.