Frequently Asked Questions

Answers to common questions about the Zebrafish Atlas.

This page is enhanced with AI-powered content that updates dynamically
Table of Contents

General Questions

What is the Zebrafish Atlas?

The Zebrafish Atlas is a comprehensive database of zebrafish microanatomy and gene expression data, designed to support research in developmental biology, genetics, and disease modeling. It provides high-resolution images of zebrafish at various developmental stages, with detailed anatomical annotations and associated metadata.

Who can use the Zebrafish Atlas?

The Zebrafish Atlas is available to researchers, educators, students, and anyone interested in zebrafish biology. Basic browsing is available to all users, while advanced features require a free account. Researcher privileges are granted to verified researchers from academic or research institutions.

Is the Zebrafish Atlas free to use?

Yes, the Zebrafish Atlas is a free resource for the scientific community. Our mission is to advance zebrafish research by providing open access to high-quality anatomical and gene expression data.

How often is the Zebrafish Atlas updated?

New data is added on an ongoing basis as researchers contribute to the atlas. Major system updates are typically released quarterly. You can view recent additions in the "What's New" section of the homepage.

Account & Access

Do I need an account to use the Zebrafish Atlas?

Basic browsing of public datasets is available without an account. To access advanced features like downloading high-resolution images, contributing data, or using the API, you'll need to create a free account.

How do I get Researcher privileges?

Researcher privileges are granted to verified members of academic and research institutions. To request Researcher status:

  1. Create an account using your institutional email address
  2. Go to Account Settings → Request Researcher Access
  3. Provide information about your research and institution
  4. Our team will review your request (typically within 1-2 business days)

I forgot my password. How do I reset it?

To reset your password:

  1. Go to the Login page
  2. Click the "Forgot Password?" link
  3. Enter your email address and click "Send Reset Link"
  4. Check your email for instructions to create a new password

Can multiple people from the same lab share an account?

No, each user should have their own individual account. This ensures proper attribution for contributions and maintains security. If your lab needs to share access to uploaded data, consider creating a lab group in the platform.

Data & Images

What types of zebrafish data are available in the atlas?

The Zebrafish Atlas contains:

  • High-resolution microscopy images at various developmental stages
  • Multiple section orientations (coronal, sagittal, transverse)
  • Anatomical structure annotations and segmentations
  • Gene expression patterns
  • Different zebrafish varieties (wildtype, transgenic, mutant)
  • MicroCT 3D reconstructions

What developmental stages are covered?

The Zebrafish Atlas includes data from multiple developmental stages, including:

  • Embryonic stages (hours post fertilization - hpf)
  • Larval stages (days post fertilization - dpf)
  • Juvenile and adult stages (months post fertilization - mpf)

The most comprehensive coverage is available for key developmental stages like 24hpf, 48hpf, 3dpf, 5dpf, and adult stages.

How do I download images for my research?

Users with Researcher privileges can download high-resolution images:

  1. Navigate to the image you want to download in the Slide Viewer
  2. Click the "Download" button in the information panel
  3. Select your preferred format (TIFF, JPEG, PNG)
  4. The image will download to your computer

For bulk downloads, use the API or contact support for assistance.

Are there restrictions on using the downloaded data?

Data from the Zebrafish Atlas is available for research and educational purposes under our Data Usage Policy. When using the data in publications or presentations, please cite the Zebrafish Atlas as described in the Research page.

Uploading & Contributing

How can I contribute data to the Zebrafish Atlas?

Researchers can contribute new data through the upload interface:

  1. Ensure you have Researcher privileges
  2. Navigate to the Upload page
  3. Follow the instructions for single or bulk uploads
  4. Provide comprehensive metadata for proper categorization
  5. Submit your data for processing

What file formats are accepted for uploads?

The Zebrafish Atlas accepts the following image formats:

  • TIFF (.tif, .tiff) - preferred for high-resolution data
  • JPEG (.jpg, .jpeg) - acceptable for web-optimized images
  • PNG (.png) - useful for images with transparency

For large datasets or specialized formats, please contact support.

Is there a size limit for uploads?

Individual file uploads are limited to 500MB per file. If you need to upload larger files, you can:

  • Use the chunked upload feature in the API
  • Contact support for assistance with very large datasets
  • Consider compression or tiling for extremely large images

How do I add annotations to my uploaded images?

After uploading an image, you can add anatomical annotations:

  1. Navigate to your uploaded image in the Slide Viewer
  2. Click the "Annotate" button in the toolbar
  3. Use the annotation tools to mark structures
  4. Select the appropriate anatomical structure for each annotation
  5. Save your annotations

For batch annotation or segmentation of multiple images, contact our team for assistance.

Technical Issues

The Slide Viewer isn't displaying images correctly. What should I do?

If you're experiencing issues with the Slide Viewer:

  1. Ensure you're using a modern browser (Chrome, Firefox, Safari, Edge)
  2. Clear your browser cache and reload the page
  3. Check your internet connection for stability
  4. Try disabling browser extensions that might interfere
  5. If problems persist, try a different browser or device

Why are some images loading slowly?

High-resolution images can be quite large, requiring time to load completely. Factors that affect loading speed include:

  • Your internet connection speed
  • The size and complexity of the image
  • Server load at time of access
  • Browser cache status

The viewer loads images progressively, so you can start exploring while higher-resolution details continue to load.

How can I report a bug or technical issue?

To report technical issues:

  1. Click the "Report Issue" button in the page footer
  2. Provide a detailed description of the problem
  3. Include steps to reproduce the issue
  4. If possible, attach screenshots or error messages
  5. Include your browser and operating system information

Our technical team will investigate and respond to your report.

Is there an offline version of the Zebrafish Atlas?

Currently, the Zebrafish Atlas is a web-based platform and requires an internet connection. However, researchers can download datasets for offline use. For research groups with limited connectivity, we can provide custom solutions - please contact support to discuss your needs.

Error: No API key available. Please contact an administrator.
Some FAQs are dynamically generated by AI based on the current database content
Last updated: 2026-10-30

Research & Citation

How should I cite the Zebrafish Atlas in my publications?

Please cite the Zebrafish Atlas as follows:

Author, A., Author, B., & Author, C. (2024). The Zebrafish Atlas: A 3D Microanatomical and Gene Expression Database for Disease Modeling. Penn State University.

When citing specific images or datasets, please include the corresponding DOI or accession number provided with each entry.

Can I use images from the Zebrafish Atlas in my publications?

Yes, images from the Zebrafish Atlas can be used in academic publications with proper attribution. Please follow these guidelines:

  • Include the standard citation (see above)
  • Acknowledge the original contributors if specified
  • Include the image's unique identifier in the figure caption
  • Follow any additional requirements specified by your publisher

Does the Zebrafish Atlas have an API for research applications?

Yes, the Zebrafish Atlas provides a comprehensive RESTful API for programmatic access. With the API, you can:

  • Query and download images and datasets
  • Access anatomical structure data
  • Retrieve metadata and annotations
  • Contribute data to the atlas

For API documentation and access, see the API Documentation.

How can I collaborate with the Zebrafish Atlas team?

We welcome collaborations with researchers and institutions. Potential collaboration opportunities include:

  • Contributing significant datasets to the atlas
  • Developing new analysis tools or visualizations
  • Integrating the atlas with other research platforms
  • Joint research projects using atlas data

To discuss collaborative opportunities, please contact our team with a brief description of your proposed collaboration.