Data Formats

Data Format Overview

The Zebrafish Atlas uses standardized data formats to organize and present zebrafish microanatomical and gene expression data. Understanding these formats is essential for effectively using and contributing to the atlas.

Primary Data Categories

• Image Data: High-resolution microscopy images in various formats
• Metadata: Descriptive information about each image
• Anatomical Structures: Hierarchical classification of zebrafish anatomy
• Segmentation Data: Structure annotations and segmentation masks

Image Formats

The Zebrafish Atlas supports multiple image formats, with different formats preferred for different use cases:

Supported Image Formats

Image Properties

Each image in the Zebrafish Atlas includes the following technical properties:

• Dimensions: Width and height in pixels
• Resolution: Physical resolution (e.g., pixels per micron)
• Bit Depth: Typically 8-bit (256 levels) or 16-bit (65,536 levels) per channel
• Channels: Number and type of channels (e.g., RGB, grayscale, fluorescence channels)
• Compression: Type of compression used, if any

Segmentation Overlays

Segmentation data is stored as separate mask layers that can be overlaid on the original images:

• Binary Masks: One mask per anatomical structure
• Label Maps: Single image with integer codes for each structure
• Contours: Vector outlines of structures

Metadata Formats

Comprehensive metadata is stored for each image in the Zebrafish Atlas, ensuring proper categorization and enabling advanced search functionality:

Core Metadata Fields

Metadata Format

Metadata is stored internally in JSON format and can be exported in several standard formats:

{
  "id": "bdc5a24e-9f3e-42f1-a53c-6c822a0f7abe",
  "title": "Zebrafish Wildtype - 24hpf - Coronal - 40x",
  "description": "24 hours post fertilization, coronal section",
  "age_type": "24hpf",
  "cut_type": "Coronal",
  "species_category": "Wildtype",
  "file_path": "uploads/24hpf/coronal/24hpf_Coronal_20240410_123456.tif",
  "thumbnail_url": "uploads/24hpf/coronal/thumbnails/24hpf_Coronal_20240410_123456.jpg",
  "segmentation_progress": 75,
  "magnification": "40x",
  "treatment": "H&E stain",
  "upload_date": "2024-04-10T12:34:56Z",
  "uploaded_by": {
    "id": "user123",
    "name": "Jane Researcher",
    "institution": "Marine Biology Institute"
  },
  "tags": ["24hpf", "coronal", "wildtype", "neural development"],
  "dimensions": {
    "width": 2048,
    "height": 1536,
    "physical_width_um": 500,
    "physical_height_um": 375
  },
  "acquisition": {
    "microscope": "Zeiss Axio Imager",
    "objective": "40x/0.75 Plan-Neofluar",
    "camera": "Zeiss Axiocam 503",
    "acquisition_date": "2024-03-15T09:30:00Z"
  }
}

Anatomical Structure Format

The Zebrafish Atlas uses a hierarchical system to represent zebrafish anatomy. This organization is based on established zebrafish anatomy ontologies with adaptations for the atlas.

Structure Data Model

Structure Hierarchy

Structures are organized in a hierarchical tree with multiple levels:

{
  "anatomical_id": 1000,
  "name": "Central Nervous System",
  "abbreviation": "CNS",
  "parent_anatomical_id": null,
  "system_path": "Central Nervous System",
  "color": "#2E86C1",
  "children": [
    {
      "anatomical_id": 1001,
      "name": "Forebrain",
      "abbreviation": "FB",
      "parent_anatomical_id": 1000,
      "system_path": "Central Nervous System/Forebrain",
      "color": "#3498DB",
      "children": [
        {
          "anatomical_id": 1002,
          "name": "Olfactory Bulb",
          "abbreviation": "OB",
          "parent_anatomical_id": 1001,
          "system_path": "Central Nervous System/Forebrain/Olfactory Bulb",
          "color": "#5DADE2",
          "children": []
        },
        // Additional structures...
      ]
    },
    // Additional structures...
  ]
}

Ontology and Taxonomy

The Zebrafish Atlas uses standardized ontologies and taxonomies to ensure interoperability with other biological databases and research tools.

Developmental Stages

Developmental stages follow standard zebrafish staging conventions:

• hpf: Hours post fertilization (e.g., 24hpf, 48hpf)
• dpf: Days post fertilization (e.g., 3dpf, 5dpf)
• mpf: Months post fertilization, often with sex specification (e.g., 3mpf_male, 3mpf_female)

Orientations

Three standard anatomical orientations are used:

• Coronal: Sections along the dorsal-ventral axis
• Sagittal: Sections along the left-right axis
• Transverse: Sections along the anterior-posterior axis

Species Categories

Several zebrafish variants and related species are included:

• Wildtype: Standard zebrafish strain
• Transgenic: Genetically modified zebrafish with fluorescent markers
• Casper: Transparent zebrafish variant
• Axolotl: Related model organism for comparative studies

Ontology Mappings

The atlas provides mappings to common ontologies:

Export Formats

The Zebrafish Atlas allows data export in various standard formats for use in other research tools and databases:

Image Export

Metadata Export

Segmentation Export

File Naming Conventions

The Zebrafish Atlas uses standardized file naming conventions to ensure consistency and easy identification of image files:

Standard Naming Pattern

AgeType_CutType_SpeciesCategory_Timestamp.extension

For example:

24hpf_Coronal_Wildtype_20240410_123456.tif
5dpf_Sagittal_Transgenic_20240411_091523.tif
3mpf_female_Transverse_Casper_20240412_153042.tif

Naming Components

Directory Structure

Files are organized in a hierarchical directory structure that mirrors the naming convention:

uploads/
├── 24hpf/
│   ├── coronal/
│   │   ├── 24hpf_Coronal_Wildtype_20240410_123456.tif
│   │   ├── 24hpf_Coronal_Transgenic_20240410_124512.tif
│   │   └── ...
│   ├── sagittal/
│   │   ├── 24hpf_Sagittal_Wildtype_20240410_130145.tif
│   │   └── ...
│   └── transverse/
│       ├── 24hpf_Transverse_Wildtype_20240410_133025.tif
│       └── ...
├── 5dpf/
│   ├── coronal/
│   │   └── ...
│   └── ...
└── 3mpf_female/
    ├── coronal/
    └── ...

Working with Zebrafish Atlas Data