Publication details

Free tools for automated cell image acquisition and analysis



Year of publication 2009
MU Faculty or unit

Faculty of Informatics

Description Centre for Biomedical Image Analysis (CBIA) of Masaryk University in Brno, Czech Republic, has been developing and implementing new methods for automated image acquisition and analysis of multi-dimensional fluorescence images of cells and their parts for over a decade. Recently, all these tools have been released for free use under GNU GPL licence. Source codes as well as binaries for Microsoft Windows and Linux platforms are available for download. The main package is called Acquiarium and supports optimized image acquisition for camera-based fluorescence microscopes, especially confocal Nipkow-disk systems. Further, it offers different types of image analysis, such as image filtering, image segmentation, object measurements, spatial arrangement studies, etc. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in 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. Another important package is simulation toolbox developed for the evaluation of algorithm correctness. For this purpose, it is best to test algorithm behavior on data with available ground truth information. Unfortunately ground truth is usually not availbale in cell imaging. Therefore we have developed a tool to generate both ground truth images (artificial objects similar to cells) as well as images of these artificial objects after passing the optical and/or electronic set-up. The latter images are the input of the algorithm. The algorithm results (e.g., segmenattaion or measurement results) are then compared to ground truth data (e.g., true boundary or true measurement values). Further tools support, for example, image data visualization, movement analysis using optical flow or database of optical components from different manufactureres together with their spectral characteristics and total light throughput evaluation. More information and download instructions are available at CBIA web pages:
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