About the atlas

Glass histology slides have long been the standard for analysis of normal, mutant, and disease microanatomy. Recent advancements in microscopy, computation, and the internet have made possible exciting new ways to share the data residing on traditional glass slides. With the introduction of slide scanning technologies, glass slides can be imaged in their entirety and saved as virtual slides in computer databases. This has set the stage for the creation of online histology atlases that enable users from around the world to share slide data.

Virtual slide technology enables users to view high-resolution imagery with a significantly reduced download time. Virtual slides are panned and magnified in a manner similar to a traditional microscope but offer constant context with respect to the remainder of the slide, labeling, comparison, and collaborative possibilities beyond the limitations of physical microscopy.

This atlas was originally constructed primarily for zebrafish and human tissues. We are seeking partners to help us find and share internationally unique slide collections that are in danger of being lost. We invite ideas and involvement from scientific and medical individuals and communities to make available unique and compelling slide collections. To this end we encourage and seek discussion with members of the scientific community for the benefit of society.

The following are the component atlases under current construction:

Zebrafish virtual slides:
The first goal was to provide infrastructure for service as a central repository for digital histological sections of normal and abnormal zebrafish tissue that allows progressive magnification and labeling in a manner that is coordinated with existing anatomical and phenotypic ontologies. The next goals for this project are to plan for scanning of slide collections, and to customize the database structure to a more scalable format.
Human and other virtual slides:
The second goal, which may become a primary goal, was to obtain slides from human anatomy and pathology for comparison with data from other model organisms. A subgoal was to establish post slides from other model systems.
MicroCT:
We are using the zebrafish to pursue the goal of 3D imaging of whole, mm-scale organisms (and later, specimens) for phenomics, the high-throughput study of phenotype. Accordingly, we have pursued a form of X-ray tomography in micron scale with cellular resolution. Using synchrotron microCT, we have created a 3-dimensional version of histology for zebrafish we are calling Pan-Cellular Tissue Tomography (PANCETTO). Our goal is to generate reconstructions from which the full animal can be visualized from 2D slices in any direction. This work is a collaboration with the La Riviere laboratory at University of Chicago and physicists at the Advanced Photon Source of Argonne National Laboratory.

Citing the Atlas

If you use images from the atlas, to help us continue our work we request the following:

  1. Cite the specific frame you are copying from using the "link to this" tool at the top right of any virtualslide.
  2. Credit https://bio-atlas.psu.edu/, NIH grant 5R24 RR01744, Jake Gittlen Cancer Research Foundation, and PA Tobacco Settlement Fund.
  3. Comparative analysis of fixation and embedding techniques for optimized histological preparation of zebrafish.
    Copper JE, Budgeon LR, Foutz CA, van Rossum DB, Vanselow DJ, Hubley MJ, Clark DP, Mandrell DT, Cheng KC.
    Comp Biochem Physiol C Toxicol Pharmacol. 2018 Jun;208:38-46.

People

Project PI
Keith Cheng
Atlas Coordinator
Jean Copper
Webmaster and
Web Resource Coordinator
Steven Peckins
Belinda Giardine
Programming
Steven Peckins
Belinda Giardine
Image processing & labeling
Steven Peckins
David Mandrell
Processing and Sectioning
Lynn Budgeon
Veterinary and Comparative Pathologist
Timothy K Cooper
3D MicroCT Images
Xuying Xin
Tim Sledz 3
Arun Tatiparthi 3
Francesco De Carlo 1
Xianghui Xiao 1
Patrick LaRiviere 2
Gordon Kindlmann 2
Bioinformatic Coordinator
Victor Canfield
Systems Administration
Penn State Univ.
Fish Facility Manager
Peggy Hubley
Past personnel
Christina Foutz (nee Wentz, past atlas coordinator)
Adam Sidor (programming)
Anthony Cheng (labeling)
Saurabha Bhatnagar (web)
Eileen Barno
Mike Abendroth
Zachary Gershenson
Darin Clark
  1. Advanced Photon Source, Argonne National Labs
  2. University of Chicago
  3. Micro Photonics, Inc., Allentown, PA

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, 1.3M]
  • 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, 4.5M]
  • 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, 559K]
  • Comparative analysis of fixation and embedding techniques for optimized histological preparation of zebrafish.Copper JE, Budgeon LR, Foutz CA, van Rossum DB, Vanselow DJ, Hubley MJ, Clark DP, Mandrell DT, Cheng KC.Comp Biochem Physiol C Toxicol Pharmacol. 2018 Jun;208:38-46.
  • 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, 1.6M]