Publication details

Acquiarium: Free Software for the Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy

Authors

MATULA Pavel MAŠKA Martin DANĚK Ondřej MATULA Petr KOZUBEK Michal

Type Article in Proceedings
Conference IEEE International Symposium on Biomedical Imaging
MU Faculty or unit

Faculty of Informatics

Citation
Web http://dx.doi.org/10.1109/ISBI.2009.5193258
Field Computer hardware and software
Keywords free software; fluorescence microscopy; image acqusition; 3D image analysis; image cytometry
Description This paper describes free software (called Acquiarium, http://cbia.fi.muni.cz/acquiarium.html) for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, the quantification and spatial arrangement of segmented objects, volume rendering, and statistical evaluation. The software is designed for the easy processing of a collection of many 3D images. It can be used for the analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. The paper gives an overview of the software and its key design ideas.
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