fix links

Author: Clare72

content/en/blog/news/neurofly2026.md

@@ -8,6 +8,6 @@ description: >
 
 The 21st Biennial European Drosophila Neurobiology Conference, NeuroFly 2026, will be held at the University of Cologne, Germany, from September 7th to 11th, 2026. This conference continues the tradition of bringing together researchers from around the world to discuss the latest advancements in Drosophila neurobiology, including studies on neuronal circuits, synapses, connectome, signal transmission, behavior, development, and more. The event emphasizes interdisciplinary interactions in an inclusive environment, featuring a mix of invited talks and abstracts from both junior and senior researchers.
 
-Virtual Fly Brain (VFB) is excited about the upcoming conference and is exploring opportunities to host a workshop/tutorial on connectomics and transcriptomics data we have available, similar to our previous successful sessions such as the one at [NeuroFly 2024](neurofly2024.md) titled 'Bridging connectomics and transcriptomics' ([workshop notebook](http://tinyurl.com/workshopVFB)). This new workshop will introduce available connectomes and transcriptomics data, highlight important differences between datasets, and demonstrate how to perform your own analysis using the latest [tools](/docs/Tutorials/APIs/Connectome/tools) and [APIs](/docs/Tutorials/APIs/) for integrating Drosophila neuroscience data. Stay tuned for updates on our participation.
+Virtual Fly Brain (VFB) is excited about the upcoming conference and is exploring opportunities to host a workshop/tutorial on connectomics and transcriptomics data we have available, similar to our previous successful sessions such as the one at [NeuroFly 2024](neurofly2024.md) titled 'Bridging connectomics and transcriptomics' ([workshop notebook](http://tinyurl.com/workshopVFB)). This new workshop will introduce available connectomes and transcriptomics data, highlight important differences between datasets, and demonstrate how to perform your own analysis using the latest [tools](/docs/past-workshops/connectome/tools) and [APIs](/docs/tutorials/apis/) for integrating Drosophila neuroscience data. Stay tuned for updates on our participation.
 
 For more information about NeuroFly 2026, including registration, abstract submission, and program details, visit the official website at [https://neurofly.org/home/](https://neurofly.org/home/) or the 2026 conference page at [https://neurofly.org/y2026/](https://neurofly.org/y2026/).

content/en/docs/APIs/_index.md

@@ -16,7 +16,7 @@ VFB provides access to its data through several APIs and databases. The core dat
 - **VFB Web Interface**: [https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto) - User-friendly web interface for browsing and querying VFB data
 
 **For Programmatic Access:**
-- **VFBconnect Library**: [https://vfb-connect.readthedocs.io/](https://vfb-connect.readthedocs.io/) - Python library that provides high-level access to VFB data and queries. See also: [VFB API Tutorial](Tutorials/APIs/0_VFB_API_overview.md)
+- **VFBconnect Library**: [https://vfb-connect.readthedocs.io/](https://vfb-connect.readthedocs.io/) - Python library that provides high-level access to VFB data and queries. See also: [VFB API Tutorial](/docs/tutorials/apis/VFB_API_overview.md)
 
 **For Advanced Data Access:**
 - **Direct APIs** (documented below): Low-level access to underlying databases and reasoning services

content/en/docs/Concepts/splits.md

@@ -12,11 +12,11 @@ Split drivers comprise at least two partial transcription factors that can recon
 
 <img src="/images/splits_images.png" max-width="50%" alt="A split-GAL4 expression pattern at the intersection of the expression patterns of two hemidrivers.">
 
-Researchers can identify split drivers for neurons of interest from the `Targeting Splits` section of a cell type [Term Info](/docs/website-features/terminfo/) page or by using [similarity scores](/docs/tutorials/website/similarityscore/) from a single neuron image. It is also possible to [search](/docs/website-features/search_query/) directly for particular hemidrivers and combinations.
+Researchers can identify split drivers for neurons of interest from the `Targeting Splits` section of a cell type [Term Info](/docs/website-features/terminfo) page or by using [similarity scores](/docs/tutorials/website/similarityscore/) from a single neuron image. It is also possible to [search](/docs/website-features/search_query) directly for particular hemidrivers and combinations.
 
 <img src="/images/splits_terminfo.png" max-width="50%" alt="Targeting Splits section of cell type Term Info page." >
 
-Similar to [non-split drivers](/docs/concepts/transgene/), VFB contains images and curated information about expression patterns for combinations. Each combination gets a standard name in VFB, reflecting the names of the component hemidrivers and any short names for the combination from the literature are added as synonyms (e.g. "[P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD} expression pattern](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=VFBexp_FBtp0123314FBtp0119891)" has_exact_synonym: SS02256").
+Similar to [non-split drivers](/docs/concepts/transgene), VFB contains images and curated information about expression patterns for combinations. Each combination gets a standard name in VFB, reflecting the names of the component hemidrivers and any short names for the combination from the literature are added as synonyms (e.g. "[P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD} expression pattern](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?id=VFBexp_FBtp0123314FBtp0119891)" has_exact_synonym: SS02256").
 
 <img src="/images/split_vfb.png" alt="split expression shown in Virtual Fly Brain (VFB)" max-width="50%" >
 

content/en/docs/Data/templates.md

@@ -7,7 +7,7 @@ description: >-
       Summary of templates on Virtual Fly Brain and the painted domains/regions available in those templates.
 ---
 
-Canonical templates not only allow for spatial alignment of image data, but also are often painted to make a reference atlas of anatomical regions. Many central nervous system (CNS) templates exist for Drosophila, below we provide a summary of those used in VFB. Templates can be downloaded from their [Term Info](../../website-features/terminfo/#data) pages.
+Canonical templates not only allow for spatial alignment of image data, but also are often painted to make a reference atlas of anatomical regions. Many central nervous system (CNS) templates exist for Drosophila, below we provide a summary of those used in VFB. Templates can be downloaded from their [Term Info](/docs/website-features/terminfo/#data) pages.
 
 ## Central Nervous System from Janelia Research Campus JRC2018
 

content/en/docs/Tutorials/APIs/VFB_API_overview.md

@@ -955,4 +955,4 @@ pd.DataFrame.from_records(KC_types)
 
 **2.2** Methods for querying connectivity
 
-Please see [Connectivity Notebook](/docs/past-workshops/connectome/4_connectomics/) for examples.
+Please see [Connectivity Notebook](/docs/past-workshops/connectome/4_connectomics) for examples.

content/en/docs/Tutorials/vfb-mcp-guide.md

@@ -358,8 +358,8 @@ VFB terms use standardized identifiers:
 ## Next Steps
 
 - **Explore the tool:** Visit [vfb3-mcp.virtualflybrain.org](https://vfb3-mcp.virtualflybrain.org/)
-- **Read more about NBLAST:** See our [NBLAST concepts page](/docs/concepts/nblast/)
-- **Learn about VFB APIs:** Check our [API overview](/docs/tutorials/apis/0_vfb_api_overview/)
+- **Read more about NBLAST:** See our [NBLAST concepts page](/docs/concepts/nblast)
+- **Learn about VFB APIs:** Check our [API overview](/docs/tutorials/apis/vfb_api_overview)
 - **Browse VFB directly:** Visit the main [Virtual Fly Brain site](https://virtualflybrain.org/)
 
 ## Common Questions
@@ -368,7 +368,7 @@ VFB terms use standardized identifiers:
 A: No, if you're using Claude or another MCP-compatible LLM with the integration already set up, just start asking questions.
 
 **Q: Can I download the data I find?**
-A: Yes, many results include links to download images, neuron skeletons, and connectivity data. Check the [API documentation](/docs/tutorials/apis/0_vfb_api_overview/) for programmatic access.
+A: Yes, many results include links to download images, neuron skeletons, and connectivity data. Check the [API documentation](/docs/tutorials/apis/vfb_api_overview) for programmatic access.
 
 **Q: What if I don't know the VFB ID?**
 A: The search tool can find terms by name or keyword. The LLM will help you locate the right term.
@@ -378,4 +378,4 @@ A: Absolutely! You can ask your LLM to retrieve VFB data and then perform additi
 
 ---
 
-**Happy exploring!** If you have questions or suggestions about the VFB MCP tool, please reach out to the [VFB team](/about/contactus/).
+**Happy exploring!** If you have questions or suggestions about the VFB MCP tool, please reach out to the [VFB team](/about/contactus).

content/en/docs/Website Features/termcontext.md

@@ -9,7 +9,7 @@ weight: 60
 ---
 <link rel="stylesheet" href="https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto/node_modules/@geppettoengine/geppetto-client/geppetto-client/style/css/gpt-icons.css">
 
-Select a graph from the [Term Info](../search_query/#ontology-terms-and-graphs) to display it in the Term Context pane. The `location` graph shows partonomy relationships, and the `classification` graph shows parentage of the selected term. Click on any term in the graph to select it and view its Term Info.
+Select a graph from the [Term Info](/docs/website-features/search_query/#ontology-terms-and-graphs) to display it in the Term Context pane. The `location` graph shows partonomy relationships, and the `classification` graph shows parentage of the selected term. Click on any term in the graph to select it and view its Term Info.
 
 <p align="center">
   <img src="/images/term-context.png" alt="Term Context tab showing classification of MBON01." style="max-width=50%" />

content/en/docs/Website Features/terminfo.md

@@ -19,7 +19,7 @@ Each entity in VFB has a unique `Name`. The `Name` field also shows semantic tag
 
 ## Ontology terms and Graphs
 
-`Classification` and `Relationships` fields show parent and related ontology classes for the selected entity. Click to navigate to the Term Info pages for these terms. The `location` and `classification` [Term Context](../termcontext) graphs show partonomy relationships and parentage of the selected entity, respectively.
+`Classification` and `Relationships` fields show parent and related ontology classes for the selected entity. Click to navigate to the Term Info pages for these terms. The `location` and `classification` [Term Context](/docs/website-features/termcontext) graphs show partonomy relationships and parentage of the selected entity, respectively.
 
 <p align="center">
   <img src="/images/terminfo/terminfo-ontologies.png" alt="Classification, Relationships and Graphs in Term Info." style="max-width=50%" />
@@ -29,13 +29,13 @@ Each entity in VFB has a unique `Name`. The `Name` field also shows semantic tag
 
 ## Data
 
-[`Thumbnails`](../thumbnails) show available images (as a carousel if multiple). These can be clicked to add the image to the 3D viewer.
+[`Thumbnails`](/docs/website-features/thumbnails) show available images (as a carousel if multiple). These can be clicked to add the image to the 3D viewer.
 
 <i class="far fa-hand-pointer"></i>   Click on thumbnails to add an image to the 3D viewer
 
-[Queries](../search_query/#queries-from-term-info) relevant to the selected entity can find related entities and other relevant information. Some EM neurons also have an option to add the neuron to the [Circuit Browser](../circuitbrowser) tool to explore connectivity data. Queries are specialised for different types of entity, for example, the Term Info page for a neuronal cell type may have queries to find images, transgene expression and transcriptomics data, whereas an EM image may have queries to find connectivity data.
+[Queries](/docs/website-features/search_query/#queries-from-term-info) relevant to the selected entity can find related entities and other relevant information. Some EM neurons also have an option to add the neuron to the [Circuit Browser](/docs/website-features/circuitbrowser) tool to explore connectivity data. Queries are specialised for different types of entity, for example, the Term Info page for a neuronal cell type may have queries to find images, transgene expression and transcriptomics data, whereas an EM image may have queries to find connectivity data.
 
-<i class="fab fa-quora"></i>   Run term related [queries](../search_query/#queries-from-term-info)
+<i class="fab fa-quora"></i>   Run term related [queries](/docs/website-features/search_query/#queries-from-term-info)
 
 Images (and citation information) can be downloaded from the `Downloads` section and their source dataset, template, and licence information can be found in their own Term Info fields.
 

content/en/docs/Website Features/thumbnails.md

@@ -6,7 +6,7 @@ weight: 55
 description: >-
      VFB (Virtual Fly Brain) thumbnails are color depth maximum projection images that allow users to visualize the distribution of intensity values across different depths in a 3D image stack. 
 ---
-Thumbnails are found in [query results](../search_query/#query_results) and on [Term Info pages](../terminfo).
+Thumbnails are found in [query results](/docs/website-features/search_query/#query_results) and on [Term Info pages](/docs/website-features/terminfo).
 
 ## VFB Thumbnail features
 

content/en/docs/past workshops/Connectome/3_Visualisation.md

@@ -1149,7 +1149,7 @@ navis.plot3d(nl, color=neuron_cmap, hover_name=True, legend_group=source_map, wi
 
 VFB has regions of interest defined for every template. These can be browsed on our template ROI browser:
 
-![png](/images/3_Visualisation_files/vfb_roi.png")
+![png](/images/3_Visualisation_files/vfb_roi.png)
 
 or the [results of queries](https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto?q=VFB_00101567,PaintedDomains) available from each template. The ROIs for JRC2018Unisex come from Janelia (the work of Kazonori Shinomiya) and align with domains on the Hemibrain following standard cross-registration.