Publication details

Algorithms and data representation in the FISH 3.0 image processing system



Year of publication 2002
Type Article in Proceedings
Conference Biophysics of the genome and its interactions
MU Faculty or unit

Faculty of Informatics

Field Use of computers, robotics and its application
Keywords image processing; automated microscopy
Description FISH 3.0 is a new client-server software system developed in the Laboratory of Optical Microscopy at the Faculty of Informatics, Masaryk University. From the technical point of view it differs from its predecessor, FISH 2.0, in the possibility to store data and analyze images on a remote server or cluster. Therefore its performance is not limited by the user's hardware and massive transfers of the 3D image data are not required. FISH 3.0 contains tools for true 3D representation of cell compounds and specific algorithms for 3D image processing. Besides that, every acquired image or a result of analysis stored in the FISH 3.0 system is linked to a dataset with all information necessary to repeat the acquisition or analysis. This contribution mainly concerns the concept of image and cell model representation used in FISH 3.0 and newly implemented algorithms for image analysis. It presents the top-level schema of data representation, FISH 3.0 data formats for 3D images, boundaries and signals, available algorithms, and practical issues concerning data management in FISH 3.0.
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