Scientific Research
Client
Clepio Biotech
Role
Lead Data and Solution Architect
OCTAVIA OME-Zarr
Scientific Imaging Framework
End-to-end architecture for OME-Zarr ingestion, PostgreSQL control, formal CSV contracts, Spark processing and Parquet Data Objects.
Architecture Flow
§ 01 Context
The platform addresses multiresolution volumetric images, Zarr and OME-NGFF metadata, segmentation labels, chunk grids, coordinate transformations, pipeline configurations, Cellpose outputs, stitched products, object-level measurements and scientific aggregates.
§ 02 Designed System
◆PostgreSQL control plane for batches, staging, audit and lineage
◆Object storage for OME-Zarr assets, CSV packages and Parquet datasets
◆Airbyte for acquisition, Airflow for orchestration
◆Python interpreters for OME-Zarr structures
◆Spark for distributed calculation and materialisation
◆Immutable CSV publication packages with manifests and SHA-256 checksums
§ 03 Capabilities
- —Expected chunk inventory computed as N_chunks = ∏ᵢ ceil(shapeᵢ / chunk_shapeᵢ)
- —Lineage and quality validation ahead of full binary payload arrival
- —Deterministic reprocessing across multiresolution levels
§ 04 Objects & Stack
Data Objects
- OME-Zarr store
- Scientific products
- Node-level metadata
- Pipeline and request configuration
- Expected chunk manifest
- Segmented objects
- Object relationships
- Segmentation aggregates
Technologies
PostgreSQLObject storageAirbyteAirflowPythonSparkParquetOME-ZarrOME-NGFF
§ 06 Related Reading
Essay 12
What Is a Data Object?
*The term Data Object is often used loosely to describe a table, file, API payload, business entity, or data product. Such ambiguity undermines the very stability the concept is intended to provide. This essay offers a rigorous definition: a Data Object is a versioned logical contract representing a coherent entity, event, state, or document-like assertion, with explicit identity, temporal semantics, attributes, relations, quality constraints, provenance, and governance. It is independent of any single source or physical storage format, though it must be implementable in concrete technologies. The essay develops a formal tuple for Data Objects, distinguishes them from source records and consumer views, and analyses granularity, lifecycle, compatibility, and ownership. Philosophically, the Data Object is treated as an institutional object: neither a natural thing nor an arbitrary schema, but a stabilised representation whose legitimacy depends on transparent rules and continued use.*
Essay 03
Determinism Is Not Repetition: The Conditions of Reproducible Data
Data platforms frequently promise that the same input will produce the same output. The promise is attractive, but often false because “the same input” is defined too narrowly. A computation depends not only on source records but on code, configuration, reference data, library versions, execution engines, clocks, seeds, policies, and hidden environmental state. This essay distinguishes repetition, determinism, reproducibility, replicability, and auditability. It formalises a data computation as a function over an extended state space, examines sources of non-determinism in distributed and temporal systems, and proposes an evidence model for reproducible outputs. The philosophical question is one of identity through time: when are two executions instances of the same computation, and when is a numerically equal result merely accidental? The essay argues that reproducibility is not achieved by rerunning code but by preserving the computational world in which a claim was produced.