Fix visium

[alexvpickering]

Description

Adds multi-sample spatial layout with metadata-based grouping in Data Exploration: samples can be grouped into rows by a sample-level metadata track (via a rewritten group-by settings panel), with a shared grid layout keeping images, segmentations, centroids, and molecules aligned. Single-sample spatial plots now cap their view to the tissue extent (reading the pipeline's originalSize) so blank padding isn't shown, and segmentation overlays render with crisp nearest-neighbour pixels. Also includes performance fixes for large experiments — cheaper cell-set union/count passes, a memoised cell-set-hierarchy selector, cached colour parsing and zarr metadata — plus hiding the tissue image by default.

Details

URL to issue

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Link to staging deployment URL (or set N/A)

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Links to any PRs or resources related to this PR

Integration test branch

master

Merge checklist

Your changes will be ready for merging after all of the steps below have been completed.

Code updates

Have best practices and ongoing refactors being observed in this PR

• Migrated any selector / reducer used to the new format.
• All new dependency licenses have been checked for compatibility.

Manual/unit testing

• Tested changes using InfraMock locally or no tests required for change, e.g. Kubernetes chart updates.
• Validated that current unit tests for code work as expected and are sufficient for code coverage or no unit tests required for change, e.g. documentation update.
• Unit tests written or no unit tests required for change, e.g. documentation update.

Integration testing

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will not pass the required status checks for merging.

• Started end-to-end tests on the latest commit.

Documentation updates

• Relevant Github READMEs updated or no GitHub README updates required.
• Relevant Wiki pages created/updated or no Wiki updates required.

Optional

• Staging environment is unstaged before merging.
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[dbmi-svc-checkmarx]

Checkmarx One – Scan Summary & Details – 4b7650e4-7f70-478f-9dc4-5736119e43f9

---

New Issues (3)

Checkmarx found the following issues in this Pull Request

#	Severity	Issue	Source File / Package	Checkmarx Insight
1		CVE-2026-62389	Npm-ws-7.4.6	details Recommended version: 7.5.0 Description: ws before 8.21.1 contains a memory exhaustion vulnerability in lib/receiver.js where the fragment guard only triggers when fragment count reaches m... Attack Vector: NETWORK Attack Complexity: LOW Vulnerable Package
2		CVE-2026-62389	Npm-ws-7.5.9	details Description: ws before 8.21.1 contains a memory exhaustion vulnerability in lib/receiver.js where the fragment guard only triggers when fragment count reaches m... Attack Vector: NETWORK Attack Complexity: LOW Vulnerable Package
3		CVE-2026-62389	Npm-ws-8.14.2	details Recommended version: 8.17.1 Description: ws before 8.21.1 contains a memory exhaustion vulnerability in lib/receiver.js where the fragment guard only triggers when fragment count reaches m... Attack Vector: NETWORK Attack Complexity: LOW Vulnerable Package

---

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[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	686.51 KB (🟡 +22 B)

Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

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Six Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/experiments/[experimentId]/data-exploration	1.51 MB (🟡 +799 B)	2.18 MB
/experiments/[experimentId]/data-processing	515.37 KB (🟡 +288 B)	1.17 MB
/experiments/[experimentId]/plots-and-tables/frequency	448.27 KB (-2 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	485.71 KB (🟡 +130 B)	1.14 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	491.6 KB (🟡 +163 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-molecules	643.98 KB (🟡 +338 B)	1.3 MB

Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

[codecov]

Codecov Report

❌ Patch coverage is 63.19018% with 60 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.02%. Comparing base (c7246a2) to head (41e674c).
⚠️ Report is 5 commits behind head on master.

Files with missing lines	Patch %	Lines
...data-exploration/spatial/createZarrArrayAdapter.js	5.55%	12 Missing and 5 partials ⚠️
...ponents/data-exploration/spatial/SpatialViewer.jsx	69.38%	15 Missing ⚠️
...ata-exploration/spatial/SpatialGroupBySettings.jsx	7.14%	13 Missing ⚠️
...components/data-exploration/spatial/loadOmeZarr.js	12.50%	6 Missing and 1 partial ⚠️
...mponents/data-exploration/spatial/bitmaskLayers.js	25.00%	5 Missing and 1 partial ⚠️
src/components/plots/useSpatialStream.js	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1067      +/-   ##
==========================================
+ Coverage   77.01%   77.02%   +0.01%     
==========================================
  Files         607      608       +1     
  Lines       14678    14763      +85     
  Branches     3670     3710      +40     
==========================================
+ Hits        11304    11371      +67     
- Misses       3160     3173      +13     
- Partials      214      219       +5     

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[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	686.52 KB (🟡 +38 B)

Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Six Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/experiments/[experimentId]/data-exploration	1.51 MB (🟡 +1022 B)	2.18 MB
/experiments/[experimentId]/data-processing	515.37 KB (🟡 +288 B)	1.17 MB
/experiments/[experimentId]/plots-and-tables/frequency	448.27 KB (-2 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	485.71 KB (🟡 +130 B)	1.14 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	491.6 KB (🟡 +163 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-molecules	643.98 KB (🟡 +338 B)	1.3 MB

Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	686.52 KB (🟡 +38 B)

Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Six Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/experiments/[experimentId]/data-exploration	1.51 MB (🟡 +1.11 KB)	2.18 MB
/experiments/[experimentId]/data-processing	515.37 KB (🟡 +288 B)	1.17 MB
/experiments/[experimentId]/plots-and-tables/frequency	448.27 KB (-2 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	485.71 KB (🟡 +130 B)	1.14 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	491.6 KB (🟡 +163 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-molecules	643.98 KB (🟡 +338 B)	1.3 MB

Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.