Software

Computational Optical Sectioning Microscopy Open Source (COSMOS) Software package


The COSM open source (COSMOS) software package is currently under development by the Computational Imaging Research Laboratory (CIRL) led by Dr. Preza. COSMOS has four platform-independent graphical user interfaces (GUIs) developed using a visualization tool kit for PSF generation, intensity estimation, image visualization and performance analysis. The estimation interface currently offers 5 different algorithms for data processing: the Depth Variant Expectation Maximization algorithm [1] , a linear least square algorithm [2] , a linear maximum a posteriori algorithm [3] , the Jansen-van Cittert algorithm [4] , and the Expectation Maximization algorithm [5] . Three out of five algorithms and the PSF generation software were available in the original XCOSM package developed for X-windows in the early 1990s and disseminated by the PI and collaborators [6] . The COSMOS package replaces the XCOSM package and provides new and upgraded capabilities which are detailed in the COSMOS user manual [7] . There are two models by which the PSFs can be generated. The user may choose either the Gibson and Lanni model [8] or the Haeberle model [9] .

USER MANUAL  | WINDOWS | MAC | LINUX | Source code

Screenshots

COSM Tool

COSM PSF

 tools  PSF

COSM Viewer

COSM Estimation

 Viewer  Estimation


References:

1. Preza, C. and Conchello, J-A., "Depth-variant maximum-likelihood restoration for three-dimensional fluorescence microscopy", J. Opt. Soc. Am. A., 21:1593-1601, 2004.
2. Preza, C., Miller, M. I., Thomas, Jr., L. J., and McNally, J. G., "Regularized linear method for reconstruction of three-dimensional microscopic objects from optical sections", J. Opt. Soc. Am. A., 9(2):219-228, 1992.
3. Preza, C., Miller, M. I., and Conchello, J.-A., "Image reconstruction for 3-D light microscopy with a regularized linear method incorporating a smoothness prior", Biomedical Image Processing and Biomedical Visualization, R. S. Acharya and D. B. Goldgof, Eds., Proc. SPIE 1905:129-139, 1993.
4, Agard, D. A., "Optical sectioning microscopy", Annu. Rev. Biophys. Bioeng., 13:191-219, 1984.
5. Conchello, J.-A., "Super-resolution and convergence properties of the expectation-maximization algorithm for maximum-likelihood deconvolution of incoherent images", J. Opt. Soc. Am. A, 15:2609-2620, 1998.
6. XCOSM software package
7. Ghosh, S., "COSMOS User Manual," Computational Imaging Research Laboratory, The University of Memphis, 2010.
8. Gibson, S. F. and Lanni, F., "Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy," J. Opt. Soc. Am. A., 9:54–66, 1992.
0. O. Haeberlé, "Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions. Part I: Conventional microscopy," Opt. Commun. 216, 55-63, 2003.