EPFL | Biomedical Imaging Group | Computational Bioimaging

Computational Bioimaging—Selected Topics

D. Sage, F. Soulez, Z. Püspöki, A. Badoual

Journée MICA 2019: Analyse d'images et bases de données (MICA'19), Valbonne, French Republic, January 22, 2019.

Recent advances in microscope technology combined with powerful computers now provide outstanding images (3D, time-lapse, multichannel, fluorescence), allowing one to address fundamental questions in developmental biology, molecular biology and neuroscience. The analysis of this unprecedented flow of imaging data requires the development of specific software tools to numerically reconstruct images and to automatically perform segmentation, quantification and tracking of structures of interest. This has led to the emergence of a new field of research, #bioimage informatics# which aims to develop computational procedures to process, analyze, and visualize light microscopy images. Here, we report our experience in the development of open-source software tools. These tools are written as Java plugins for the popular open-source software suites: ImageJ, Fiji or Icy. We address the following topics with are common problems in computational bioimaging: the 3D microscopy deconvolution, the directional image analysis for detecting filament-like structure, the deformable model (snake) for segmentation, and the tracking of bright spots in noisy images.

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