Overview
The SynDB data platform is accessible through the API. By search, you may find and download analysis-ready connectomics tables and derived metrics; by upload, you may share your data to become part of a meta-analytical study.
Composition
The SynDB data platform is designed to provide a comprehensive and organized repository of high-resolution microscopy data products and associated metadata. In practice, SynDB is organized around three components: Metadata, Analysis-Ready Tables, and Optional Source Assets.
Metadata
The metadata is used to define and retrieve datasets. It stores metadata about the data in the respective dataset:
- Brain region
- Sourcing model animal
- Genetic manipulations (mutations)
- Microscopy method
- Publication information
The metadata is defined by the data owner during upload.
Warning
Dataset
You must split your dataset into individual SynDB datasets if any of these fields differ within your own dataset.
Analysis-ready tables
The primary data in SynDB is not the raw microscopy volume. It is the analysis-ready output derived from that volume: neuron tables, synapse tables, compartment metrics, and other object-level measurements that can be searched and analyzed directly. Each neuronal compartment and structure has its own schema in SynDB.
To facilitate efficient data management, every row is linked to a dataset via its ID. This linkage enables robust search capabilities by filtering through metadata, without requiring users or ETL jobs to move terabytes of raw imaging data around. You can learn more about how dataset metadata filtration works in the article on search.
The flexible data model of SynDB supports this functionality by defining specific parameters for each compartment and structure. These varied tables are unified into comprehensive datasets through dataset metadata, which effectively organizes data groups across the platform.
Optional source assets
SynDB can also attach source-linked assets such as meshes and SWC skeleton files when they are available. These assets are optional and supplement the tabular release. SynDB does not require contributors to hand over raw imaging volumes or segmentation stores in order to ingest a dataset.
Organization & Tracking
- Collections & Tags: Group datasets into curated collections and apply tags for discovery.
- Provenance & Citations: Track version history, data lineage, and generate citations in BibTeX/RIS format. Export metadata as JSON-LD for linked data integration.