1. Structure
  2. Arrays
  3. Foundation
  4. Key Concepts
  5. Storage
  6. Fragment Metadata
  • Home
  • What is TileDB?
  • Get Started
  • Explore Content
  • Accounts
    • Individual Accounts
      • Apply for the Free Tier
      • Profile
        • Overview
        • Cloud Credentials
        • Storage Paths
        • REST API Tokens
        • Credits
    • Organization Admins
      • Create an Organization
      • Profile
        • Overview
        • Members
        • Cloud Credentials
        • Storage Paths
        • Billing
      • API Tokens
    • Organization Members
      • Organization Invitations
      • Profile
        • Overview
        • Members
        • Cloud Credentials
        • Storage Paths
        • Billing
      • API Tokens
  • Catalog
    • Introduction
    • Data
      • Arrays
      • Tables
      • Single-Cell (SOMA)
      • Genomics (VCF)
      • Biomedical Imaging
      • Vector Search
      • Files
    • Code
      • Notebooks
      • Dashboards
      • User-Defined Functions
      • Task Graphs
      • ML Models
    • Groups
    • Marketplace
    • Search
  • Collaborate
    • Introduction
    • Organizations
    • Access Control
      • Introduction
      • Share Assets
      • Asset Permissions
      • Public Assets
    • Logging
    • Marketplace
  • Analyze
    • Introduction
    • Slice Data
    • Multi-Region Redirection
    • Notebooks
      • Launch a Notebook
      • Usage
      • Widgets
      • Notebook Image Dependencies
    • Dashboards
      • Dashboards
      • Streamlit
    • Preview
    • User-Defined Functions
    • Task Graphs
    • Serverless SQL
    • Monitor
      • Task Log
      • Task Graph Log
  • Scale
    • Introduction
    • Task Graphs
    • API Usage
  • Structure
    • Why Structure Is Important
    • Arrays
      • Introduction
      • Quickstart
      • Foundation
        • Array Data Model
        • Key Concepts
          • Storage
            • Arrays
            • Dimensions
            • Attributes
            • Cells
            • Domain
            • Tiles
            • Data Layout
            • Compression
            • Encryption
            • Tile Filters
            • Array Schema
            • Schema Evolution
            • Fragments
            • Fragment Metadata
            • Commits
            • Indexing
            • Array Metadata
            • Datetimes
            • Groups
            • Object Stores
          • Compute
            • Writes
            • Deletions
            • Consolidation
            • Vacuuming
            • Time Traveling
            • Reads
            • Query Conditions
            • Aggregates
            • User-Defined Functions
            • Distributed Compute
            • Concurrency
            • Parallelism
        • Storage Format Spec
      • Tutorials
        • Basics
          • Basic Dense Array
          • Basic Sparse Array
          • Array Metadata
          • Compression
          • Encryption
          • Data Layout
          • Tile Filters
          • Datetimes
          • Multiple Attributes
          • Variable-Length Attributes
          • String Dimensions
          • Nullable Attributes
          • Multi-Range Reads
          • Query Conditions
          • Aggregates
          • Deletions
          • Catching Errors
          • Configuration
          • Basic S3 Example
          • Basic TileDB Cloud
          • fromDataFrame
          • Palmer Penguins
        • Advanced
          • Schema Evolution
          • Advanced Writes
            • Write at a Timestamp
            • Get Fragment Info
            • Consolidation
              • Fragments
              • Fragment List
              • Consolidation Plan
              • Commits
              • Fragment Metadata
              • Array Metadata
            • Vacuuming
              • Fragments
              • Commits
              • Fragment Metadata
              • Array Metadata
          • Advanced Reads
            • Get Fragment Info
            • Time Traveling
              • Introduction
              • Fragments
              • Array Metadata
              • Schema Evolution
          • Array Upgrade
          • Backends
            • Amazon S3
            • Azure Blob Storage
            • Google Cloud Storage
            • MinIO
            • Lustre
          • Virtual Filesystem
          • User-Defined Functions
          • Distributed Compute
          • Result Estimation
          • Incomplete Queries
        • Management
          • Array Schema
          • Groups
          • Object Management
        • Performance
          • Summary of Factors
          • Dense vs. Sparse
          • Dimensions vs. Attributes
          • Compression
          • Tiling and Data Layout
          • Tuning Writes
          • Tuning Reads
      • API Reference
    • Tables
      • Introduction
      • Quickstart
      • Foundation
        • Data Model
        • Key Concepts
          • Indexes
          • Columnar Storage
          • Compression
          • Data Manipulation
          • Optimize Tables
          • ACID
          • Serverless SQL
          • SQL Connectors
          • Dataframes
          • CSV Ingestion
      • Tutorials
        • Basics
          • Ingestion with SQL
          • CSV Ingestion
          • Basic S3 Example
          • Running Locally
        • Advanced
          • Scalable Ingestion
          • Scalable Queries
      • API Reference
    • AI & ML
      • Vector Search
        • Introduction
        • Quickstart
        • Foundation
          • Data Model
          • Key Concepts
            • Vector Search
            • Vector Databases
            • Algorithms
            • Distance Metrics
            • Updates
            • Deployment Methods
            • Architecture
            • Distributed Compute
          • Storage Format Spec
        • Tutorials
          • Basics
            • Ingestion & Querying
            • Updates
            • Deletions
            • Basic S3 Example
            • Running Locally
          • Advanced
            • Versioning
            • Time Traveling
            • Consolidation
            • Distributed Compute
            • RAG LLM
            • LLM Memory
            • File Search
            • Image Search
            • Protein Search
          • Performance
        • API Reference
      • ML Models
        • Introduction
        • Quickstart
        • Foundation
          • Basics
          • Storage
          • Cloud Execution
          • Why TileDB for Machine Learning
        • Tutorials
          • Ingestion
            • Data Ingestion
              • Dense Datasets
              • Sparse Datasets
            • ML Model Ingestion
          • Management
            • Array Schema
            • Machine Learning: Groups
            • Time Traveling
    • Life Sciences
      • Single-cell
        • Introduction
        • Quickstart
        • Foundation
          • Data Model
          • Key Concepts
            • Data Structures
            • Use of Apache Arrow
            • Join IDs
            • State Management
            • TileDB Cloud URIs
          • SOMA API Specification
        • Tutorials
          • Data Ingestion
          • Bulk Ingestion Tutorial
          • Data Access
          • Distributed Compute
          • Basic S3 Example
          • Multi-Experiment Queries
          • Appending Data to a SOMA Experiment
          • Add New Measurements
          • SQL Queries
          • Running Locally
          • Shapes in TileDB-SOMA
          • Drug Discovery App
        • Spatial
          • Introduction
          • Foundation
            • Spatial Data Model
            • Data Structures
          • Tutorials
            • Spatial Data Ingestion
            • Access Spatial Data
            • Manage Coordinate Spaces
        • API Reference
      • Population Genomics
        • Introduction
        • Quickstart
        • Foundation
          • Data Model
          • Key Concepts
            • The N+1 Problem
            • Architecture
            • Arrays
            • Ingestion
            • Reads
            • Variant Statistics
            • Annotations
            • User-Defined Functions
            • Tables and SQL
            • Distributed Compute
          • Storage Format Spec
        • Tutorials
          • Basics
            • Basic Ingestion
            • Basic Queries
            • Export to VCF
            • Add New Samples
            • Deleting Samples
            • Basic S3 Example
            • Basic TileDB Cloud
          • Advanced
            • Scalable Ingestion
            • Scalable Queries
            • Query Transforms
            • Handling Large Queries
            • Annotations
              • Finding Annotations
              • Embedded Annotations
              • External Annotations
              • Annotation VCFs
              • Ingesting Annotations
            • Variant Statistics
            • Tables and SQL
            • User-Defined Functions
            • Sample Metadata
            • Split VCF
          • Performance
        • API Reference
          • Command Line Interface
          • Python API
          • Cloud API
      • Biomedical Imaging
        • Introduction
        • Foundation
          • Data Model
          • Key Concepts
            • Arrays
            • Ingestion
            • Reads
            • User Defined Functions
          • Storage Format Spec
        • Quickstart
        • Tutorials
          • Basics
            • Ingestion
            • Read
              • OpenSlide
              • TileDB-Py
          • Advanced
            • Batched Ingestion
            • Chunked Ingestion
            • Machine Learning
              • PyTorch
            • Napari
    • Files
  • API Reference
  • Self-Hosting
    • Installation
    • Upgrades
    • Administrative Tasks
    • Image Customization
      • Customize User-Defined Function Images
      • AWS ECR Container Registry
      • Customize Jupyter Notebook Images
    • Single Sign-On
      • Configure Single Sign-On
      • OpenID Connect
      • Okta SCIM
      • Microsoft Entra
  • Glossary
  1. Structure
  2. Arrays
  3. Foundation
  4. Key Concepts
  5. Storage
  6. Fragment Metadata

Fragment Metadata

arrays
foundation
fragments
fragment metadata
Each fragment of an array contains metadata about the fragment, including the number of cells, the file offsets, and aggregate and indexing information.

Each fragment includes a special fragment metadata file inside its folder. This files contains necessary index information about the fragment for TileDB to implement efficient read operations. Some of the information the fragment metadata file stores includes:

  • The number of total cells in the fragment.
  • The file offsets of each data tile for each attribute and dimension.
  • Aggregate information for each data tile.
  • Indexing information (such as the R-tree in sparse arrays).

For more information about the format of the fragment metadata file, visit the Storage Format Spec section.

Over time, the number of fragments in an array increases with each write you perform, which may have a negative impact on performance. To reduce these effects, TileDB supports consolidation of fragments, as well as fragment metadata. Consolidation of fragment metadata generates a consolidated fragment metadata file, which combines the metadata of multiple fragments in one, significantly boosting the read performance.

Fragments
Commits