A novel framework for Z-registration of electron microscopy image stacks

J Konetschnig, Kurt Saetzler, P Elbischger

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    Recent developments in electron microscopy (EM) indicate that focused ion beam (FIB) in combination with field emission scanning electron microscopy (FESEM) presents promising results in capturing the structure Nanogold R marked histones within mitotic chromosomes. In order to compute a three-dimensional density map of their distribution within the chromosome, the generated image series has to be registered. This work introduces a new registration framework built into OpenCAR, a novel open source software for three dimensional reconstruction of biological structures. The scaleinvariant feature transform (SIFT) is used for identifying landmarks within the images. A modified random sample consensus (RANSAC) algorithm then optimizes the transformation model using the generated landmarks. The registration framework is evaluated using serial block-face scanning electron microscopy (SBFSEM) images of neuronal structures as ground truth for accuracy evaluation and FIB/FESEM images of chromosomes are used for repeatability assessment. Delivering promising results in aligning FIB/FESEM image stacks, the proposed method offers an excellent framework for assisting in the 3D reconstruction process of EM image series.
    LanguageEnglish
    Title of host publicationUnknown Host Publication
    Pages89-96
    Number of pages8
    Publication statusPublished - May 2010
    Event34th Workshop of the Austrian Association for Pattern Recognition (AAPR/ÖAGM'10) - Zwettl, Waldviertel, Austria
    Duration: 1 May 2010 → …

    Conference

    Conference34th Workshop of the Austrian Association for Pattern Recognition (AAPR/ÖAGM'10)
    Period1/05/10 → …

    Fingerprint

    Electron microscopy
    Focused ion beams
    Chromosomes
    Field emission
    Scanning electron microscopy

    Cite this

    Konetschnig, J., Saetzler, K., & Elbischger, P. (2010). A novel framework for Z-registration of electron microscopy image stacks. In Unknown Host Publication (pp. 89-96)
    Konetschnig, J ; Saetzler, Kurt ; Elbischger, P. / A novel framework for Z-registration of electron microscopy image stacks. Unknown Host Publication. 2010. pp. 89-96
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    Konetschnig, J, Saetzler, K & Elbischger, P 2010, A novel framework for Z-registration of electron microscopy image stacks. in Unknown Host Publication. pp. 89-96, 34th Workshop of the Austrian Association for Pattern Recognition (AAPR/ÖAGM'10), 1/05/10.

    A novel framework for Z-registration of electron microscopy image stacks. / Konetschnig, J; Saetzler, Kurt; Elbischger, P.

    Unknown Host Publication. 2010. p. 89-96.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

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    AB - Recent developments in electron microscopy (EM) indicate that focused ion beam (FIB) in combination with field emission scanning electron microscopy (FESEM) presents promising results in capturing the structure Nanogold R marked histones within mitotic chromosomes. In order to compute a three-dimensional density map of their distribution within the chromosome, the generated image series has to be registered. This work introduces a new registration framework built into OpenCAR, a novel open source software for three dimensional reconstruction of biological structures. The scaleinvariant feature transform (SIFT) is used for identifying landmarks within the images. A modified random sample consensus (RANSAC) algorithm then optimizes the transformation model using the generated landmarks. The registration framework is evaluated using serial block-face scanning electron microscopy (SBFSEM) images of neuronal structures as ground truth for accuracy evaluation and FIB/FESEM images of chromosomes are used for repeatability assessment. Delivering promising results in aligning FIB/FESEM image stacks, the proposed method offers an excellent framework for assisting in the 3D reconstruction process of EM image series.

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    Konetschnig J, Saetzler K, Elbischger P. A novel framework for Z-registration of electron microscopy image stacks. In Unknown Host Publication. 2010. p. 89-96