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5 changes: 4 additions & 1 deletion config.toml
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Expand Up @@ -109,7 +109,10 @@ section = ["HTML", "print", "RSS"]
[privacy.disqus]
disable = false
[privacy.googleAnalytics]
anonymizeIP = false
# anonymizeIP is a no-op for GA4 (Universal Analytics-era flag) but is set
# to true here to signal intent — GA4 itself transiently uses the IP for
# geolocation only and does not store it. See content/en/about/cookies.md.
anonymizeIP = true
disable = false
respectDoNotTrack = true
useSessionStorage = true
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8 changes: 4 additions & 4 deletions content/en/_index.html
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Expand Up @@ -22,15 +22,15 @@

<p>
<b style="color:red">
<span> <a href="https://flybase.org/" target="_blank">Our colleagues at FlyBase needs your help!</a> </span>
<span> <a href="https://flybase.org/" target="_blank">Our colleagues at FlyBase need your help!</a> </span>
</b>
</p>
<p>
<b>
Because of recent changes to government funding, the NIH grant that supported <a href="https://flybase.org/" target="_blank">FlyBase</a> has been terminated.
They are now reaching out to the community for emergency funding. Please click here for more information and to contribute:
Because of changes to US government funding, the foreign subaward of the NHGRI grant that supported the <a href="https://flybase.org/" target="_blank">FlyBase</a> curation team at the University of Cambridge has been terminated.
They are now reaching out to the community to assist with funding. Please click here for more information and to contribute:
<a href="https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase" target="_blank">Contribute to FlyBase wiki page</a>
Thank you in advance for your support to keep FlyBase on air and continuing to serve the Drosophila research community.
Thank you in advance for your support in allowing FlyBase to continue serving the Drosophila research community.
We remain grateful to Wellcome for their continued support of Virtual Fly Brain.
</b>
</p>
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74 changes: 74 additions & 0 deletions content/en/about/accessibility.md
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@@ -0,0 +1,74 @@
---
title: "Accessibility Statement"
linkTitle: "Accessibility"
weight: 22
---

## Accessibility statement for Virtual Fly Brain

Website accessibility statement in line with the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018.

This statement applies to the public Virtual Fly Brain (VFB) services hosted at [www.virtualflybrain.org](https://www.virtualflybrain.org) and its sub-domains. VFB is run by the [University of Edinburgh's School of Informatics](https://www.inf.ed.ac.uk/) as a research data integration platform for *Drosophila melanogaster* neurobiology.

The University of Edinburgh is committed to making its websites and applications accessible in line with the regulations. This website is partially compliant with the [Web Content Accessibility Guidelines (WCAG) 2.2 AA standard](https://www.w3.org/TR/WCAG22/), with the non-compliances listed below.

We want as many people as possible to be able to use this website. Where the underlying content is inherently visual (3D image stacks, neuron skeletons and connectivity diagrams) we recognise that some features cannot be made fully accessible without losing scientific meaning, and we have documented those limitations below.

### Using this website

Across the site you should be able to:

- Change colours, contrast levels and font size using your browser settings on the documentation pages
- Use the documentation pages without encountering flashing, scrolling or moving content
- Listen to most of the documentation pages with a screen reader (JAWS, NVDA, VoiceOver)
- Navigate the documentation pages by keyboard alone
- Resize text up to 200% on the documentation pages without loss of content

The 3D web client (Geppetto-based) and the embedded CATMAID connectome viewers have known accessibility limitations — see below.

### Customising the website

[AbilityNet — My Computer My Way](https://mcmw.abilitynet.org.uk/) has advice on making your device easier to use if you have a disability.

### Known accessibility issues

#### Non-compliance with WCAG 2.2 AA criteria

- **1.1.1 Non-text content.** Not all neuron images and anatomical diagrams have meaningful alternative text.
- **1.3.1 Info and relationships, 1.3.2 Meaningful sequence.** Some legacy figure pages do not present content in a programmatically determined reading order.
- **1.4.1 Use of colour.** Some neuroanatomical schematics use colour as the sole means of distinguishing regions or cell types.
- **1.4.3 Contrast (minimum).** Some embedded figures from external publications use low-contrast labels we cannot modify.
- **2.1.1 Keyboard.** The Geppetto 3D viewer cannot be navigated by keyboard alone for full feature parity with mouse interaction.
- **4.1.2 Name, role, value.** The 3D viewer's scene-graph elements (neurons, brain regions) are not exposed to assistive technology as named, role-tagged elements.

#### Content that is not within the scope of the accessibility regulations

- **Third-party scientific content.** PDFs and figures imported from peer-reviewed publications retain their original formatting, including small text size and low colour contrast, and are republished under their original licences. We do not modify them.
- **The CATMAID connectome viewers (`*.catmaid.virtualflybrain.org`)** are embedded third-party software whose interface is optimised for mouse and keyboard interaction at high zoom levels. We do not control its accessibility behaviour.
- **Older content (pre-September 2018).** Some legacy pages and PDFs pre-date the regulations and are kept for reference; we will replace them with accessible HTML where reasonable.

#### Ongoing improvements

- Adding `aria-label` and image-map fallbacks to anatomical schematics.
- Documenting alternative routes to the same information (text search, the [VFB_connect Python API](https://github.com/VirtualFlyBrain/VFB_connect), and the [VFB MCP server](https://virtualflybrain.org/blog/2026/02/07/introducing-the-vfb-model-context-protocol-mcp-tool/)) so users who cannot use the 3D viewer can still access the underlying data programmatically.
- Reviewing and improving alternative text for image content.
- Following the [University of Edinburgh accessibility guidance](https://www.ed.ac.uk/about/website/accessibility) for the documentation site framework.

### Feedback and contact information

If you need information from this site in a different format, or you encounter an accessibility problem we have not listed:

- Email: [support@virtualflybrain.org](mailto:support@virtualflybrain.org)
- GitHub: file an issue at [github.com/VirtualFlyBrain/VFB2/issues](https://github.com/VirtualFlyBrain/VFB2/issues)

We will respond within five working days.

### Enforcement procedure

The Equality and Human Rights Commission (EHRC) is responsible for enforcing the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018. If you are not satisfied with how we respond to your complaint, you can contact the [Equality Advisory and Support Service (EASS)](https://www.equalityadvisoryservice.com/).

### Preparation of this statement

This statement was prepared in May 2026, it has not been independently audited.

This article was published on 2026-05-19.
1 change: 1 addition & 0 deletions content/en/about/contributors.md
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Expand Up @@ -71,6 +71,7 @@ img {
[![actions-user](https://avatars.githubusercontent.com/u/65916846?v=4&s=100)](https://github.com/actions-user)
[![NeZanyat](https://avatars.githubusercontent.com/u/1211953?v=4&s=100)](https://github.com/NeZanyat)
[![afonsobspinto](https://avatars.githubusercontent.com/u/19196034?v=4&s=100)](https://github.com/afonsobspinto)
[![Copilot](https://avatars.githubusercontent.com/in/1143301?v=4&s=100)](https://github.com/apps/copilot-swe-agent)
[![snyk-bot](https://avatars.githubusercontent.com/u/19733683?v=4&s=100)](https://github.com/snyk-bot)
[![leechuck](https://avatars.githubusercontent.com/u/362161?v=4&s=100)](https://github.com/leechuck)
[![MiguelAngelRG](https://avatars.githubusercontent.com/u/12188797?v=4&s=100)](https://github.com/MiguelAngelRG)
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54 changes: 54 additions & 0 deletions content/en/about/cookies.md
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---
title: "Cookies"
linkTitle: "Cookies"
weight: 21
---

## Cookies used by Virtual Fly Brain

**Last updated: May 2026**

This page lists the cookies set by [www.virtualflybrain.org](https://www.virtualflybrain.org) and the related Virtual Fly Brain (VFB) services. It complements the [Privacy Notice](/about/privacy/).

### What is a cookie?

A cookie is a small text file that a website saves on your device when you visit. Cookies let a site recognise your browser between requests and on return visits.

### Strictly necessary cookies

These cookies are required for the website and applications to work and cannot be turned off through any opt-out mechanism without breaking core features.

| Name | Set by | Purpose | Expires |
|------|--------|---------|---------|
| `JSESSIONID` | Geppetto (`v2.virtualflybrain.org` and variants) | Maintains your application session in the 3D web client — currently selected neurons, layer visibility and camera state. | End of browser session |

### Performance cookies

These cookies help us understand how visitors use Virtual Fly Brain so we can improve content, navigation and the underlying data integrations. The data is aggregated and is not used to identify individual users.

#### Google Analytics 4

We use Google Analytics 4 (GA4), a web analytics service provided by Google LLC. GA4 receives your IP address transiently for geolocation purposes, derives an approximate location (city/country level), and discards the raw IP — it is not stored against your analytics record. The data we see is aggregated counts, paths through the site, and broad geographic distribution.

| Name | Purpose | Expires |
|------|---------|---------|
| `_ga` | Distinguishes browsers across visits. | 2 years from your most recent visit |
| `_ga_K7DDZVVXM7` | Maintains GA4 session state for the VFB property. | 2 years from your most recent visit |

For details of Google's processing, see [Google's Privacy & Terms](https://policies.google.com/privacy).

International transfer note: Google may process GA4 data on servers in the United States. The transfer is covered by the EU-U.S. Data Privacy Framework (Commission Implementing Decision (EU) 2023/1795); Google is certified under the framework. The UK extension to the framework applies for UK-origin data.

### How to opt out

You can opt out of Google Analytics on every site you visit by installing Google's [Analytics Opt-out browser add-on](https://tools.google.com/dlpage/gaoptout). You can also clear or block individual cookies via your browser's settings; doing so will not prevent you from using the public VFB services, but the Geppetto session cookie above is needed for the 3D viewer.

### Other cookies set by sites we link to

Pages elsewhere on virtualflybrain.org may embed content from third-party services (for example, YouTube or X/Twitter). Those embeds may set their own cookies; please refer to the third party's own cookie or privacy policy for details. We do not set non-essential third-party cookies of our own beyond Google Analytics.

### Contact

Questions about cookies on this site: <data@virtualflybrain.org>.

Wider University data-protection enquiries: [University of Edinburgh Data Protection Officer](mailto:dpo@ed.ac.uk).
23 changes: 13 additions & 10 deletions content/en/about/privacy.md
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Expand Up @@ -6,22 +6,23 @@ weight: 20

## Virtual Fly Brain Privacy Notice

**Last updated: February 2026**
**Last updated: May 2026**

The Virtual Fly Brain (VFB) project is committed to protecting your privacy and keeping you informed about how your personal information is used. This privacy notice explains how we collect, use, and protect your personal data when you visit our website.

### What information do we collect?

We collect information about your visit to our website through Google Analytics, a web analytics service provided by Google, Inc. This includes:
**Website analytics (Google Analytics 4).** We use Google Analytics 4 to understand how the site is used. When you visit a page, your IP address is sent to Google for the purpose of deriving an approximate geographic location, and is then discarded; the raw IP is not stored against your analytics record. The data we receive is aggregated and includes:

- Your IP address (anonymized)
- Approximate geographic location (city/country level)
- Browser type and version
- Operating system
- Referring website
- Pages visited and time spent on each page
- Geographic location (country/city level only)

We do not collect any personally identifiable information such as names, email addresses, or contact details unless you voluntarily provide them (for example, through our contact forms or feedback mechanisms).
**Web-server logs.** Our front-end load balancers and application containers produce request logs that include your IP address. These logs are short-lived and operational only — they are not persisted beyond the lifetime of the running container and are lost on restart.

We do not collect personally identifiable information such as names, email addresses or contact details unless you voluntarily provide them through our contact forms, feedback links or community channels.

### How do we use this information?

Expand All @@ -31,13 +32,13 @@ The information collected helps us:
- Improve the user experience and content
- Identify technical issues
- Analyze website traffic patterns
- Support our research by understanding user interests in neuroanatomical data
- Understand user interests in our neuroanatomical data

### Cookies and Website Privacy
### Cookies

We use Google Analytics cookies to collect this information. These are small text files stored on your device. You can control cookies through your browser settings, and you can opt out of Google Analytics tracking by visiting [Google Analytics Opt-out](https://tools.google.com/dlpage/gaoptout).
Google Analytics 4 sets cookies on your browser to distinguish your visits. The Geppetto 3D web client sets a session cookie to maintain application state during a visit. A full list of cookies set by Virtual Fly Brain, with their purposes and expiry, is on the [Cookies page](/about/cookies/), which also explains how to opt out of Google Analytics.

For more information about Google's privacy practices, please see [Google's Privacy Policy](https://policies.google.com/privacy).
For Google's processing details see [Google's Privacy & Terms](https://policies.google.com/privacy).

### Legal Basis for Processing

Expand All @@ -48,7 +49,9 @@ Our processing of your personal data is based on:

### Data Sharing and Disclosure

We do not sell, rent, or trade your personal information. Information collected by Google Analytics may be processed by Google on servers located in the United States. Google is committed to complying with the EU-U.S. Privacy Shield framework.
We do not sell, rent or trade your personal information.

Analytics data collected by Google Analytics may be processed by Google on servers located in the United States. International transfers are covered by the EU-U.S. Data Privacy Framework (Commission Implementing Decision (EU) 2023/1795); Google is [certified under the framework](https://www.dataprivacyframework.gov/list). The UK extension to the framework applies for UK-origin data.

### Data Retention

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8 changes: 7 additions & 1 deletion content/en/blog/news/VFB_MCP_Tool.md
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@@ -1,7 +1,7 @@
---
title: "Introducing the VFB Model Context Protocol (MCP) Tool"
linkTitle: "VFB MCP Tool Launch"
date: 2026-02-07
date: 2026-06-21
description: >
Explore Virtual Fly Brain data directly through your favorite LLM with the new VFB Model Context Protocol (MCP) tool - now available at vfb3-mcp.virtualflybrain.org
---
Expand Down Expand Up @@ -53,3 +53,9 @@ This tool democratizes access to VFB's complex neuroanatomical data, making it a
Check out our new [**VFB MCP Tutorial**](/docs/tutorials/vfb-mcp-guide/) for detailed guidance on using the tool, example queries, and best practices for exploring VFB data through your favorite LLM.

The VFB MCP tool represents an exciting new frontier in how researchers interact with neuroanatomical databases. We hope it accelerates your discoveries about *Drosophila* neurobiology!

## Now described in a preprint

The tool and its evaluation are now described in a preprint: McLachlan et al. (2026), *VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase*, bioRxiv. [doi:10.64898/2026.06.16.732577](https://doi.org/10.64898/2026.06.16.732577).

Benchmarked on 30 neuroscience tasks, an LLM equipped with the VFB MCP produced precise, verifiable and appropriately quantified answers on 25/30 tasks, against 14/30 for a web-search-assisted LLM and 2/30 for a bare LLM (Wilcoxon *p* < 0.01, Holm-corrected across all pairwise comparisons). The advantage was largest where answers required data quantification — 89% of those tasks were answered correctly with the MCP, against 11% with web search — reflecting the precision that VFB's expert-curated, ontology-backed knowledge graph brings to the recently integrated connectomes. The MCP server code is available at [VirtualFlyBrain/VFB3-MCP](https://github.com/VirtualFlyBrain/VFB3-MCP).
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Expand Up @@ -28,6 +28,8 @@ description: >
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<area shape="rect" coords="250,590,360,625" target="_blank" href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00101567&id=FBbt_00051239" title="left asymmetrical body (AB(L))">
<area shape="rect" coords="211,620,250,655" target="_blank" href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00101567&id=FBbt_00003680" title="nodulus (NO)">
<area shape="rect" coords="118,725,193,765" target="_blank" href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00101567&id=FBbt_00051240" title="right asymmetrical body (AB(R)) — text label">
<area shape="rect" coords="275,725,348,765" target="_blank" href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00101567&id=FBbt_00051239" title="left asymmetrical body (AB(L)) — text label">
<area shape="rect" coords="450,400,555,470" target="_blank" href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00101567&id=FBbt_00003679" title="fan-shaped body (FB) — lateral view">
<area shape="rect" coords="555,500,650,565" target="_blank" href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00101567&id=FBbt_00003678" title="ellipsoid body (EB) — lateral view">
<area shape="rect" coords="615,600,700,645" target="_blank" href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?i=VFB_00101567&id=FBbt_00003680" title="nodulus (NO) — lateral view">
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