The Daphnia Project

Our Mission

Daphnia magna, a freshwater crustacean, has been widely used as invertebrate model in aquatic toxicology and environmental monitoring. Its small size, simple anatomical organization, yet high sensitivity to toxicity makes it a perfect research model, but it is lacking a reference atlas. To fill this gap, we are creating whole-organism atlas utilizing 2D and 3D imaging. This atlas at cellular resolution will serve as a foundation for the characterization of tissue and cellular change in Daphnia.

Anatomical Reference

Histology Atlas

Here we present The Daphnia anatomical reference atlas. To provide an interactive web-based resource, we utilize 40x digital histology scans in three orthogonal planes overlaid with ontologically and anatomically informed annotations.

Wide-Field Micro-CT

Whole-Organism Phenotyping

Micro-Computed Tomography (micro-CT) is rapidly becoming commonplace in biological applications where the generation of high resolution, isotropic, 3D datasets is useful for both qualitative and quantitative phenotyping as well as visualization. While there is a fairly wide selection of commercial micro-CT scanners, optimization of sample preparation and scanning parameters can require a larger and more specialized setup than what is readily available. The focus of the Micro-CT Project is to construct and continuously develop a system that optimizes high (cellular) resolution while maintaining a large field of few. The resulting images will allow us to determine both the composition and health of individuals in samples using phenotyping tools.

Daphnia Research Group

A web-based histology atlas for the freshwater Cladocera species Daphnia magna (RRID:SCR_024913)

Version 1.0.0

Description

Whole organism atlas utilizing 2D and 3D imaging. Atlas at cellular resolution serves as foundation for characterization of tissue and cellular change in Daphnia.

Usage

Terms of Use

This work is licensed under a Creative Commons Attribution 4.0 International License as of December 1, 2023.

Citation

Resource Name: Daphnia Atlas
Version: 1.0.0
Research Resource Identifier (RRID): RRID:SCR_024913
Dataset citation: A web-based histology atlas for the freshwater Cladocera species Daphnia magna, version 1.0.0
Paper citation A web-based histology atlas for the freshwater Cladocera species Daphnia magna
Mee S. Ngu, Daniel J. Vanselow, Carolyn R. Zaino, Alex Y. Lin, Jean E. Copper, Margaret J. Beaton, Luisa Orsini, John K. Colbourne, Keith C. Cheng, Khai C. Ang
bioRxiv 2022.03.09.483544v4; DOI:10.1101/2022.03.09.483544

Support

These materials are provided as-is, without direct support.

Acknowledgements

The Team

Project Coordinator
Mee S. Ngu, PhD


Developer
Daniel J. Vanselow

Annotation
Mee S. Ngu, PhD
Carolyn R. Zaino

Principal Investigators
Khai C. Ang, PhD
Keith C. Cheng, MD PhD

Slide Scanning
Jean Copper

Histology Processing
Mee S. Ngu, PhD
Debra A. Shearer
Chadwick Harris

Contact Us
Mee S. Ngu: msn21@psu.edu
Khai C. Ang: kca2@psu.edu



Funding


Jake Gittlen Laboratories for Cancer Research

Penn State Human Health and Environment Seed Grant supported by Pennsylvania Department of Health Commonwealth Universal Research Enhancement Program Grant.
The Department of Health specifically disclaims responsibility for any analyses, interpretations, or conclusions.