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51 Publications

Showing 31-40 of 51 results
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    Saalfeld LabSinger Lab
    05/28/15 | BigDataViewer: visualization and processing for large image data sets.
    Pietzsch T, Saalfeld S, Preibisch S, Tomancak P
    Nature Methods. 2015 May 28;12(6):481-3. doi: 10.1038/nmeth.3392
    04/02/15 | Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.
    Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P
    Elife. 2015;4:. doi: 10.7554/eLife.05003

    mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3'UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT, enables the transition from mechanistic dissection of singular mRNA localization events towards global understanding of how mRNAs transcribed in the nucleus distribute in cells.

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    11/25/14 | Post-acquisition image based compensation for thickness variation in microscopy section series.
    Hanslovsky P, Bogovic JA, Saalfeld S
    IEEE International Symposium on Biomedical Imaging. 2014 Nov 25:507-11

    Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.

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    11/15/12 | ImgLib2--generic image processing in Java.
    Pietzsch T, Preibisch S, Tomancak P, Saalfeld S
    Bioinformatics. 2012 Nov 15;28(22):3009-11. doi: 10.1093/bioinformatics/bts543

    SUMMARY: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins.

    AVAILABILITY: ImgLib2 is licensed under BSD. Documentation and source code are available at and in a public repository at

    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.


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    10/24/12 | Advanced Programming with ImgLib2
    Pietzsch T, Preibisch S, Tomancak P, Saalfeld S
    Proceedings of the ImageJ User and Developer Conference. 2012 Oct 24:
    10/24/12 | ImgLib2—Generic Image Processing in Java
    Saalfeld S, Pietzsch T, Tomancak P, Preibisch S
    ImageJ User and Developer Conference. 2012 Oct 24:
    10/24/12 | Introduction to ImgLib2
    Preibisch S, Pietzsch T, Myers E, Tomancak P, Saalfeld S
    Proceedings of the ImageJ User and Developer Conference. 2012 Oct 24:
    Cardona LabSaalfeld LabFetter Lab
    07/01/12 | Elastic volume reconstruction from series of ultra-thin microscopy sections.
    Saalfeld S, Fetter RD, Cardona A, Tomancak P
    Nature Methods. 2012 Jul;9(7):717-20. doi: 10.1038/nmeth.2072

    Anatomy of large biological specimens is often reconstructed from serially sectioned volumes imaged by high-resolution microscopy. We developed a method to reassemble a continuous volume from such large section series that explicitly minimizes artificial deformation by applying a global elastic constraint. We demonstrate our method on a series of transmission electron microscopy sections covering the entire 558-cell Caenorhabditis elegans embryo and a segment of the Drosophila melanogaster larval ventral nerve cord.

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    Cardona LabSaalfeld Lab
    07/01/12 | Fiji: an open-source platform for biological-image analysis.
    Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez J, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A
    Nature Methods. 2012 Jul;9(7):676-82. doi: 10.1038/nmeth.2019

    Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

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    Saalfeld LabCardona Lab
    06/19/12 | TrakEM2 software for neural circuit reconstruction.
    Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ
    PLoS One. 2012;7(6):e38011. doi: 10.1371/journal.pone.0038011

    A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.

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