POC: bring viv-dicomweb-test work into SLIM and add basic bulk annotations support by igoroctaviano · Pull Request #381 · ImagingDataCommons/slim

igoroctaviano · 2026-04-08T00:46:20Z

Summary

POC port of viv-dicomweb-test into SLIM: Viv + Deck.gl slide viewing on dedicated /viv/... routes plus bulk simple annotations (polygons) wired through the same DICOMweb + DMV decode path as OpenLayers.

DMV: feat: export bulk annotation and graphic-fetch APIs for Viv / non-OpenLayers consumers dicom-microscopy-viewer#237

What changed (vs `master`)

Verified against feat/viv-loader ↔ master in the Slim repo (18 files, ~4.3k insertions).

Routing: New React Router paths that mirror existing case URLs but prefix /viv: /viv/studies/:studyInstanceUID/* and the GCP Healthcare store variant. ParametrizedCaseViewer passes isVivRoute and optional vivSettings from config when the pathname starts with /viv/.
src/viv/ module: dicomLoader.ts (DICOMweb tiling + DMV integration), VivSlideViewport.tsx, loadBulkAnnotationLayers.ts, vivDisplayDefaults.ts, README.md. Includes request abort/cancel handling and viewport work (incl. 8-bit SM tile positioning).
UI integration: CaseViewer.tsx switches the slide viewport to VivSlideViewport on Viv routes, adds VivSettingsDrawer and an annotation rail wired to AnnotationGroupList, and adjusts study URLs so navigation stays under /viv/….
Dependencies: @deck.gl/*, @vivjs/layers, @vivjs/loaders, @luma.gl/*; dicomweb-client raised to ^0.11.2 (plus types/dicomweb-client). Overrides pin Deck versions; bun.lock updated.
Build: craco.config.js — Babel transpilation for node_modules under @deck.gl, @luma.gl, @math.gl, @probe.gl, @hms-dbmi/viv.
DICOM web client hook: DicomWebManager.applyToPrimaryDicomwebClient so Viv tiles can attach to the primary store’s requestHooks (same XHR pipeline as VolumeImageViewer).
Config types: AppConfig.d.ts — optional vivSettings (selections, channelsVisible, contrastLimits, colors, initialViewState). There is no useViv flag; Viv is strictly /viv/... URLs.
ICC profiles: iccProfilesPreference.ts and updates in SlideViewer.tsx so ICC enable/disable persists (fixes ICC behavior with the Viv path).
Types: types/dicom-microscopy-viewer/index.d.ts extended for DMV APIs the Viv loader uses.
App.tsx: registers the Viv routes.

Branch & local setup

SLIM branch: feat/viv-loader.
POC still expects a linked dicom-microscopy-viewer checkout with Viv-facing API changes until a matching release is published. From DMV (correct branch): bun link. From the Slim checkout: bun link dicom-microscopy-viewer, then bun install if needed. bun unlink dicom-microscopy-viewer in Slim restores registry installs. Details: src/viv/README.md.

How to test

Add this server URL: https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb
Open the Viv-prefixed study URL (same study/series as before, /viv after the origin):

http://localhost:3000/viv/studies/2.25.106918873973188798943205935727506273925/series/1.3.6.1.4.1.5962.99.1.1088146757.1503397867.1637470719301.2.0
(Optional) In public/config/*.js, set vivSettings for channel/contrast/colors/initialViewState on /viv/....
Toggle annotation group visibility. Expect a long first pass while every polygon is built (~23 s in one run); after that, pan/zoom stays responsive and memory behaved better than earlier OpenLayers attempts for this POC.

Possible TODO's

deepsource-io · 2026-04-08T00:47:10Z

DeepSource Code Review

We reviewed changes in f726405...d0f9fef on this pull request. Below is the summary for the review, and you can see the individual issues we found as inline review comments.

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PR Report Card

Overall Grade	Security Reliability Complexity Hygiene

Code Review Summary

Analyzer	Status	Updated (UTC)	Details
JavaScript		Aug 14, 2026 4:52p.m.	Review ↗

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…/viv-loader

igoroctaviano · 2026-04-14T18:39:04Z

@fedorov, now you can test this using /viv
e.g.
Compare http://localhost:3000/viv/studies/2.25.302737996345872783571112300080988167697/series/1.3.6.1.4.1.5962.99.1.1354739488.2060999382.1637737312032.2.0
with http://localhost:3000/studies/2.25.302737996345872783571112300080988167697/series/1.3.6.1.4.1.5962.99.1.1354739488.2060999382.1637737312032.2.0

…/viv-loader

…into feat/viv-loader

fedorov · 2026-05-07T15:07:03Z

@igoroctaviano it would be helpful to indicate somewhere (in the "info" panel perhaps?) whether given instance is using viv or not.

I deployed the viewer with useViv: true at https://andrey-slim-test.web.app/studies/2.25.147491078891690248552488589436202370211/series/1.3.6.1.4.1.5962.99.1.1471805016.1464679391.1637854377560.2.0, and I have no clue if it worked and what backend is being used!

igoroctaviano · 2026-05-07T15:15:05Z

PR description outdated. Just use the viv route before /studies

…/viv-loader

sonarqubecloud · 2026-05-07T15:44:59Z

Quality Gate passed

Issues
46 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
2.4% Duplication on New Code

See analysis details on SonarQube Cloud

github-actions · 2026-08-14T12:16:06Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T13:00:41Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

- Return undefined explicitly in useEffect (VivBulkAnnotationLoadIndicator) - Simplify boolean returns and rename short variables (iccProfilesPreference) - Rename short variables to descriptive names (vivBulkLodPreference, dicomLoader) - Use template literal for worker source (centerOutAnnotationOrder) - Reorder variable declarations to avoid used-before-defined (centerOutAnnotationOrder) - Add skipcq for valid patterns (CaseViewer default import, void operator) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T13:26:42Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

- Reorder settle/onMessage/onError to fix used-before-defined (JS-0357) - Rename short variables: v→viewerRecord, m→affineMatrix, b→imageBits, s→imageSpp, r→ratio for JS-C1002 - Add explicit return at end of _ensureTileDecodeReady (JS-0045) - Change SyntheticDyadicPixelSource.getRaster to use Promise.reject (JS-0116) - Add skipcq comments for intentional patterns (JS-0105, JS-R1005) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T13:37:44Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

- Use function declarations instead of let+assignment for hoisting (JS-0242) - Rename short variables: v→indexValue, o→api, r→result (JS-C1002) - Add skipcq for dcmjs namespace import (JS-C1003) - Add skipcq for high-complexity functions (JS-R1005) - Use regular strings instead of template literals where no interpolation (JS-R1004) - Use property shorthand for annotationGroupWrapper (JS-0240) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T13:45:00Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

- Replace Math.random() with crypto.getRandomValues() for retry jitter (S2245) - Remove identical conditional branches in isMultipart check (S3923) - Remove unnecessary void operators in useEffect dependencies (S3735) - Extract duplicate ensureCapacity to createPayloadBuffer helper (S4144) - Add skipcq comment for getRaster interface compliance (JS-0105) - Convert template strings without interpolations to regular strings (JS-R1004) - Rename single-letter variables to descriptive names (JS-C1002) - Remove unnecessary async keyword from function returning promise (JS-0116) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T14:33:10Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

The e2e visual regression workflow is for testing bulk annotation rendering, which belongs in the feat/bump-dmv-bulk-ann branch (PR #405), not in this viv-loader branch. This branch doesn't have the e2e test infrastructure (build:e2e, test:e2e scripts). Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Remove e2e-visual.yml workflow (belongs in PR #405, not this branch) - Add skipcq for void operator usage (JS-0098) - Add skipcq for high complexity functions (JS-R1005): - buildPointLayersFromGraphicData - buildPathLayersFromGraphicData - loadBulkAnnotationMetadataAndJobs - Rename short variables (JS-C1002): - g→typedGeom, t→geomType - b→bulkApi - d→typedDataset - Use regular strings instead of template literals (JS-R1004) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T14:41:52Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

- Move skipcq comment directly above void statement (JS-0098) - Fix more template strings without interpolation (JS-R1004) - Remove async from deprecated function that doesn't await (JS-0116) - Add skipcq for buildStyledBulkOverlayLayers complexity (JS-R1005) - Rename `a` to `alpha` for opacity calculation (JS-C1002) - Add skipcq for delete statements on ref-tracked dynamic keys (JS-0320) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T14:48:50Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

Add skipcq comments for void statements (JS-0098), delete operations on dynamic keys (JS-0320), and cleanup function returns (JS-0045). Rename short variable names: a -> alpha, g -> geom (JS-C1002). Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T14:52:36Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

- Add skipcq for delete operations in loops (JS-0320) - Add skipcq for useEffect cleanup functions (JS-0045) - Rename short variables: r -> obj, w/h -> width/height, z -> tileZ, a/b -> spacingX/spacingY, t -> ratio/factor (JS-C1002) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T14:56:11Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

- Rename short variables: d -> displayOpts, w/h -> width/height, v -> viv, z -> zoom, t -> tgt (JS-C1002) - Add skipcq for void statements on fire-and-forget async ops (JS-0098) - Add skipcq for useEffect cleanup functions (JS-0045) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions · 2026-08-14T15:00:59Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

The lockfile was missing the entry for dicomweb-client@0.10.3 which is a transitive dependency from dicom-microscopy-viewer. This caused CI failures with ERR_PNPM_LOCKFILE_MISSING_DEPENDENCY. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

sonarqubecloud · 2026-08-14T16:52:37Z

Quality Gate passed

Issues
52 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.3% Duplication on New Code

See analysis details on SonarQube Cloud

github-actions · 2026-08-14T16:54:14Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

igoroctaviano added 10 commits April 7, 2026 11:16

Add viv loader

f2926c5

Improve viewport displaying

de332d5

Fixing 8-bit: Rendering images correctly (wrong position)

f7ebea7

Fixing 8-bit: Rendering images correctly (correct position)

42dbd68

Add request abort

b2dad70

Working: Bulk ann (polygons)

29d36d1

Working: Bulk ann (polygons)

457f48e

Linting

bd5bd55

Linting and padding

3fd745d

Linting and padding and styling

4fd23eb

igoroctaviano requested a review from fedorov April 8, 2026 00:54

igoroctaviano added 2 commits April 14, 2026 14:53

Merge branch 'master' of github.com:ImagingDataCommons/slim into feat…

c03494a

…/viv-loader

Fix icc profile for viv mode

d4decc8

igoroctaviano added 3 commits April 14, 2026 15:39

Merge branch 'master' into feat/viv-loader

5f0ea90

Merge branch 'master' of github.com:ImagingDataCommons/slim into feat…

c231a79

…/viv-loader

Merge branch 'feat/viv-loader' of github.com:ImagingDataCommons/slim …

3277448

…into feat/viv-loader

Merge branch 'master' of github.com:ImagingDataCommons/slim into feat…

d136f1d

…/viv-loader

igoroctaviano added 8 commits May 7, 2026 14:02

Improve performance

13bdd9a

Improve performance

a39ec69

Add logging and chunk annotations processing

d76573d

Load images from center outwards

a3147c4

Load annotations from center

74973e5

Use points to improve memory usage

93987de

Scale points

0614d09

Hardening

6b131ba

igoroctaviano added 2 commits August 14, 2026 08:07

Merge branch 'master' into feat/viv-loader

33cd2c5

Merge master into feat/viv-loader

90a43e5

Merge branch 'master' into feat/viv-loader

41e7e83

igoroctaviano and others added 3 commits August 14, 2026 11:15

fix(viv): add eslint-disable for intentional useMemo dependencies

b2c9e34

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

fix(viv): place eslint-disable before dependency array

48c5e57

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

igoroctaviano and others added 2 commits August 14, 2026 11:36

igoroctaviano and others added 2 commits August 14, 2026 13:44

Merge branch 'master' into feat/viv-loader

94ca784

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Summary

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igoroctaviano commented Apr 8, 2026 •

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