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About the Zebrafish Atlas

Background/Vision

The Zebrafish Atlas was created to answer a community call for a comprehensive, web-based, anatomical and pathological atlas of the zebrafish, which has become one of the most widely used vertebrate animal models globally. The experimental strengths of zebrafish as a model system have made it useful for a wide range of investigations addressing the missions of the NIH and NSF.

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Scanning & Image Processing

For digitizing histology slides, we purchased a Scanscope T2 scanner from Aperio Technologies, Inc. This system allows us to scan at both 20x and 40x magnification. We can scan entire slides or sections of slides and can scan up to 120 slides in a batch mode with the T2's robotic device.

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3D Reconstructions

We are producing 3D reconstructions from serial plastic sections of zebrafish embryos and larvae (Moorman lab).

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People/Credits

    Project PIs
  • Keith Cheng (oversight, 2D)
  • Steven Moorman (ontology, 3D)
    Atlas Coordinator
  • Jean Copper
    Webmaster and
    Web Resource Coordinator
  • Steven Peckins
  • Saurabha Bhatnagar
    Programming
  • Steven Peckins
  • Adam Sidor
    Image processing & labeling
  • Anthony Cheng (coordinator)
  • Saurabha Bhatnagar
  • Eileen Barno
  • Mike Abendroth
  • Zachary Gershenson
    3D MicroCT Images
  • Darin Clark
  • Tim Sledz
  • Arun Tatiparthi
    Bioinformatic Coordinator
  • Victor Canfield
    3D Reconstructions
  • Stephen Moorman (team leader)
    Fish Facility Manager
  • Peggy Hubley
    Processing and Sectioning
  • Lynn Budgeon
    ZFIN Coordinators
  • Judy Sprague
  • Melissa Heindel
    Server
  • Vijay Agarwala
  • Jason Holmes
    Past personnel
  • Christina Foutz (nee Wentz), past atlas coordinator

References/papers

  • Mohideen M-APK, Beckwith LG, Tsao-Wu GS, Moore JL, Wong ACC, Chinoy MR, Cheng KC. Histology-based screen for zebrafish mutants with abnormal cell differentiation. Developmental Dynamics 228:414-423, 2003. PMID: 14579380 [View PDF]
  • Sabaliauskas NA, Foutz CA, Mest JR, Budgeon LR, Sidor A, Gershenson J, Joshi S, Cheng KC. High-throughput zebrafish histology. Methods 39:246-254, 2006. PMID: 16870470 [View PDF]
  • Tsao-Wu GS, Weber CH, Budgeon LR, Cheng KC. Agarose embedded tissue arrays for histologic and genetic analysis. Biotechniques 25:614-618, 1998. PMID: 9793642 [View PDF]
  • Tsao-Wu GS, Weber CH, Budgeon LR, Cheng KC. Agarose embedded tissue arrays for histologic and genetic analysis. In Expression Genetics: High-Throughput Methods, Chapter 4, M. McClelland and A. Pardee (eds.), Eaton Publishing, pp. 31-36, 1999. [View PDF]