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Bioimage Informatics: Image-Processing Algorithms and Life-Science Applications

D. Sage

International Neuroinformatics Coordinating Facility (Belgian Node) Training in Neuroinformatics 2013: Imaging the Brain at Different Scales—How to Integrate Multi-Scale Structural Information? (INCF-TN'13), Antwerp, Kingdom of Belgium, September 2-6, 2013.



In this presentation, we first give an overview of the underlying concepts of the image processing including: basic elements of digital signal-processing theory, pixelwise operations, digital filtering and an introduction to image analysis. Then, we show how the image-processing algorithms can be efficiently implemented as Java plugins for the open-source platform ImageJ/Fiji for the benefit of the research community.

We cover the image preparation (correction for drift by intensity-based registration, correction for photobleaching, correction for non-uniform illumination), the image restoration (extended depth-of-field procedure, denoising, 3D microscopy deconvolution), the image analysis (feature identification, segmentation, active contour, directional image analysis) and tracking of biological fluorescent particles (spot tracking).

The presentation includes intuitions and concepts of algorithms, their implementations running as ImageJ/Fiji plugins and applications to biological microscopic images.

This is joint work with members of the Biomedical Imaging Group at the EPFL who have contributed to this effort over the years.


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AUTHOR="Sage, D.",
TITLE="Bioimage Informatics: {I}mage-Processing Algorithms and
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BOOKTITLE="International Neuroinformatics Coordinating Facility
        ({B}elgian Node) Training in Neuroinformatics 2013: {I}maging the
        Brain at Different Scales---{H}ow to Integrate Multi-Scale
        Structural Information? ({INCF-TN'13})",
YEAR="2013",
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address="Antwerp, Kingdom of Belgium",
month="September 2-6,",
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