Integrate NIfTI overlay support#237
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- Introduced optional NIfTI segmentation table configuration in `app.yml` and `app-config.yml`. - Implemented new API endpoints for fetching NIfTI overlay metadata and files. - Updated handlers and query builders to support NIfTI overlay functionality. - Enhanced documentation in the deployment notebook regarding NIfTI integration.
- Updated documentation to clarify feature gating based on pixels_table and NIFTI_SEGMENTATION_TABLE. - Refactored table resolution logic to derive NIfTI table from pixels_table cookie or environment variable. - Improved error handling for cases when no valid table configuration is available.
…ns/pixels into feature/nifti_integration
…ricks-industry-solutions/pixels into feature/nifti_integration
…ns/pixels into feature/nifti_integration
dmoore247
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Jul 10, 2026
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Please confirm PR has been a full install tested, end to end, starting from nothing.
Big question what happens if feature is on (by default) and NIFTI_SEGMENTATION table is not loaded. Possible 404 error.
| WHERE study_instance_uid = %(study)s | ||
| AND series_instance_uid = %(series)s | ||
| AND (status IS NULL OR status <> 'archived') | ||
| ORDER BY version DESC NULLS LAST, created_at DESC |
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No limit to # rows returned. The client has a limit of 25?
| WHERE study_instance_uid = %(study)s | ||
| AND series_instance_uid = %(series)s | ||
| AND id = %(id)s | ||
| LIMIT 1 |
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No order by so it is indeterministic as to which one would be returned.
| valueFrom: "sql_warehouse" | ||
| - name: "DATABRICKS_PIXELS_TABLE" | ||
| value: "{PIXELS_TABLE}" | ||
| - name: "NIFTI_SEGMENTATION_TABLE" |
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On by default, chance that upon fresh deploy, code will hit 404 until is populated.
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This PR addresses a key item on the roadmap by introducing native NIfTI (Neuroimaging Informatics Technology Initiative) integration into the Pixels solution accelerator. Previously focused on DICOM imaging datasets, this expansion allows the framework to scale, ingest, and process NIfTI data formats directly within the Databricks Data Intelligence Platform.
Key Changes
NIfTI Ingestion Pipeline: Extends Pixels' parallel processing framework to parse, read, and ingest NIfTI format imaging data (.nii / .nii.gz).
Metadata & Property Extraction: Enables seamless extraction of NIfTI-specific headers, dimensional properties, and coordinate information to map them into Delta Lake tables for fast, downstream Spark SQL metadata analytics.
Pipeline Enhancements: Introduces underlying utilities to cleanly handle, extract, and convert neuroimaging file streams alongside the existing DICOM processing architecture.
Example notebook available here: notebooks/nifti/IRCAD Sample Data Loader.ipynb
Sample file used: ircad_e01_package.tar.gz