Quick Start Guide
Get started with the Zebrafish Atlas in just a few minutes.
Introduction
Welcome to the Zebrafish Atlas! This quick start guide will help you get up and running with our platform in just a few minutes. 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.
Most Popular Developmental Stages
- 30hpf (3 images)
- 36hpf (2 images)
- 24mpf_male (2 images)
- 3dpf (2 images)
- 3mpf_female (1 images)
This guide is intended for new users who want to quickly learn the basic features. For more detailed information, please refer to the specific documentation sections.
Account Setup
To get started with the Zebrafish Atlas, you'll need to create an account:
- Visit the Sign Up page
- Enter your email address and create a password
- Verify your email address by clicking the link sent to your inbox
- Complete your profile by adding your research affiliation and research interests
Users with institutional email addresses (.edu, .ac, .gov, etc.) will receive faster verification for research privileges.
User Roles
The Zebrafish Atlas has different user roles with varying access levels:
- Viewer: Can browse and view all public datasets
- Researcher: Can download high-resolution images and raw data, and contribute data
- Admin: Has full access to site administration and management features
New accounts start with Viewer privileges. To request Researcher status, please contact our support team with details about your research.
Browsing Data
The Zebrafish Atlas organizes data by developmental stage, orientation, and anatomical structures:
Navigating the Data Table
From the Data Table page, you can:
- Browse zebrafish images organized by developmental stages
- Filter images by orientation (Coronal, Sagittal, or Transverse)
- See segmentation progress for each developmental stage
- Access detailed slide information by clicking on a specific image
Developmental stages are organized chronologically from hours post fertilization (hpf) to days post fertilization (dpf) to months post fertilization (mpf).
Viewing Slides
The Zebrafish Atlas features a powerful slide viewer for examining zebrafish microanatomy:
Slide Viewer Features
- Zoom and Pan: Use the mouse wheel to zoom and click-and-drag to pan
- Toggle Information Panel: Click the info button to show/hide metadata
- Navigation: Use the arrows to move between slides in a series
- Home: Click the home button to reset the view
Image Metadata
Each slide contains rich metadata, including:
- Developmental stage
- Orientation (cut type)
- Species category
- Magnification
- Treatment information
- Segmentation progress
If you're looking for specific anatomical structures, check the segmentation progress indicator. Fully segmented images (100%) have complete anatomical labeling.
Uploading Data
Researchers can contribute to the Zebrafish Atlas by uploading their own data:
Upload Requirements
- Researcher account privileges
- High-quality images in TIFF, JPG, or PNG format
- Complete metadata for proper categorization
Upload Process
- Navigate to the Upload page
- Select the appropriate developmental stage, orientation, and species category
- Add magnification and treatment information if applicable
- Choose your image file(s) - single upload or bulk upload options are available
- Click "Upload" to submit your data
By uploading data to the Zebrafish Atlas, you agree to our Terms of Use and data sharing policies. Please ensure you have the rights to share the data you upload.
Next Steps
Now that you're familiar with the basics of the Zebrafish Atlas, you might want to explore:
- Detailed user registration information
- Advanced navigation techniques
- Our API for programmatic access
- Best practices for using the atlas in research
If you have any questions, please don't hesitate to contact our support team.