CATMAID: Collaborative Annotation Toolkit for Massive Amounts of Image Data

Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomančák

Supplementary Material

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Serial section Transmission Electron Microscopy (TEM)
Part of the Drosophila first instar larval brain serial section data set imaged with TEM consisting of 6885 (85 sections each 9×9 mosaic) tiles. Created and automatically registered with TrakEM2.
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TEM and confocal laser scanning synchronized navigation
Part of the Drosophila first instar larval brain imaged with TEM at 11,000× magnification (2.34nm/px) and confocal laser scanning microscopy stained with nirvana2, repo and sytox. Created and manually registered with TrakEM2.
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Confocal 3D-stitching comparison
Drosophila larval nervous system stained with three dyes, stitched from a grid of 2×3 RGB images compared to stacks overlaid based on microscope coordinates. We thank James W. Truman from Janelia Farm Research Campus for kindly providing the data.
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Large confocal mosaic
A zone in the dorsal telencephalon of human embryonic tissue from week 17 post conception, imaged using a 63×/1.4 objective on Zeiss LSM 510 equipped with a motorized stage (24 image stacks arranged in a 4×6 grid). We thank Simone Fietz from the lab of Wieland B. Huttner at the MPI-CBG for kindly providing the images.
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High throughput RNA in situ image data
A composite of 2500 Drosophila embryo images stained for gene expression patterns by RNA in situ hybridization. We show here 63 genes from cluster 27R enriched for early embryonic expression patterns in the mesoderm anlagen. The images are arranged linearly, grouped by gene (first image of a gene is labeled with the gene name) and ordered by developmental stage. For details see Tomancak et.al. Global analysis of patterns of gene expression during Drosophila embryogenesis Genome Biology 2007, 8(7):R145
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Poster: On-line annotation-tool for collaborative mapping of the Drosophila first instar larval brain with synapse-resolution
Presented at the European Drosophila Research Conference 2007, Vienna.
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Poster: As-rigid-as-possible registration of serial section TEM mosaics
Presented at the conference “What Can Computer Vision Do for Neuroscience and Vice Versa?”, 2008, Janelia Farm Research Campus.

Contact

Pavel Tomančák

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden, Germany

phone +49 351 210-2670
fax+49 351 210-1389

tomancak@mpi-cbg.de

© 2009 Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomančák