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Cell type contributions - #18

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Clare72 wants to merge 239 commits into

Robbie1977:masterfrom

VirtualFlyBrain:cell_type_contributions

Closed

Cell type contributions#18
Clare72 wants to merge 239 commits into
Robbie1977:masterfrom
VirtualFlyBrain:cell_type_contributions

Commits on Jul 27, 2026
- Merge pull request #413 from VirtualFlyBrain/fix/takemura-citation-year
  Robbie1977
  authored
  963e214
Commits on Aug 4, 2026
- Updating contributions from GitHub
  jenkins
  committed
  00cadee
- Restructure Templates page: per-template sections with descriptions, FlyBase references and collapsible painted-domain lists
  
  Clare72
  and
  claude
  committed
  b674d16
- Remove L1 larval CNS section from Templates page
  
  Clare72
  and
  claude
  committed
  a3b436b
Commits on Aug 5, 2026
- Rename cascade._target to cascade.target
  Robbie1977
  committed
  b99fdba
- Fix malformed ref shortcode in the workshop index
  Robbie1977
  committed
  bd44308
- Add vfb-nova, a second presentation layer for the site
  Robbie1977
  committed
  4e9b4f5
- WIP: anatomical hero — real fly body and VFB CNS meshes
  Robbie1977
  committed
  3ffd12c
- Place brain and VNC separately, per Hartenstein stage figures
  Robbie1977
  committed
  43e4d6a
- Face the fly towards the camera and hold the appendages back
  Robbie1977
  committed
  606b2d9
- Fit the CNS to the body cavities instead of guessing axes
  Robbie1977
  committed
  0384f6e
- Size the CNS by true conversion, not by filling the cavity
  Robbie1977
  committed
  9ecce7f
- Allow the hero framing to be overridden alongside the angle
  Robbie1977
  committed
  41bd7a2
- Fix VNC rotation and brain inversion
  Robbie1977
  committed
  d9df3d9
- Assign CNS axes explicitly; stop ranking the cavity
  Robbie1977
  committed
  3a215f8
- Lateral view with the head on the left; VNC forward in the thorax
  Robbie1977
  committed
  18286b6
- Replace Docsy with vfb-nova as the site's only theme
  Robbie1977
  committed
  b6f020e
- Publish via a staging build and rsync, not in place
  Robbie1977
  committed
  e8793c2
- Publish the builder image from this repo, not docsy-builder
  Robbie1977
  committed
  58b7d00
- Pin the builder to Hugo 0.164.0 and fix the compose working directory
  
  Robbie1977
  and
  claude
  committed
  3548d7c
- Set HUGO_CACHEDIR and WORKDIR in the builder image
  
  Robbie1977
  and
  claude
  committed
  6eebb97
- Fix the builder image workflow before it is ever activated
  
  Robbie1977
  and
  claude
  committed
  5c295db
- Activate the builder image workflow
  Robbie1977
  committed
  bec0567
- Merge pull request #414 from VirtualFlyBrain/feature/vfb-nova-theme
  Robbie1977
  authored
  22843cf
- Build with --noBuildLock and clear a stale lock first
  
  Robbie1977
  and
  claude
  committed
  c0ced5d
Commits on Aug 11, 2026
Commits on Aug 12, 2026
- Pin the builder to Hugo 0.122.0, the last version that completes this build
  Robbie1977
  committed
  e9019ed
- Merge pull request #418 from VirtualFlyBrain/pin-builder-hugo-0.122
  Robbie1977
  authored
  d64185a
Commits on Aug 14, 2026
Commits on Aug 15, 2026
- Reserve nav space on .page and source hero stats from the content report
  Robbie1977
  committed
  2d3c82f
- Merge pull request #422 from VirtualFlyBrain/feature/vfb-nova-hero-anatomy
  Robbie1977
  authored
  ba3133a
- Rewrite the Data section around what the knowledge base actually holds
  Robbie1977
  committed
  2a275ec
- Credit the hero body model, and lift the silhouette out of the background
  Robbie1977
  committed
  980d733
- Merge pull request #423 from VirtualFlyBrain/fix/page-nav-offset-and-content-report-stats
  Robbie1977
  authored
  fc58f70
- Update the FlyBase funding appeal to the March 2026 position
  
  Robbie1977
  authored and
  claude
  committed
  ae6a250
- Merge pull request #424 from VirtualFlyBrain/fix/hero-body-visibility-and-credit
  Robbie1977
  authored
  78a6de9
- Merge pull request #425 from VirtualFlyBrain/fix/flybase-funding-march-2026
  Robbie1977
  authored
  c9ca95d
- Correct FlyBase notice wording on the homepage
  Robbie1977
  committed
  3af172e
- List LM datasets grouped by data provider
  Robbie1977
  committed
  1844b2c
- Add FlyLight dataset table
  Robbie1977
  committed
  1261bb3
- Add VDRC provider page
  Robbie1977
  committed
  329427e
- Add FlyCircuit provider page
  Robbie1977
  committed
  6e57d13
- Add BrainTrap provider page
  Robbie1977
  committed
  4422304
- Add page for datasets with no recorded source
  Robbie1977
  committed
  98961ab
- Add contributing laboratories page with imaging sources from the papers
  Robbie1977
  committed
  04efdd5
- Narrow no-source page to datasets with no images loaded
  Robbie1977
  committed
  ff5f1d5
- Add Janelia-sourced datasets identified from release papers
  Robbie1977
  committed
  f0af329
- Update provider overview after paper-based attribution
  Robbie1977
  committed
  bd3a0f8
- Merge pull request #427 from VirtualFlyBrain/claude/lm-datasets-by-provider
  Robbie1977
  authored
  d899aab
- Merge pull request #426 from VirtualFlyBrain/claude/flybase-notice-wording
  Robbie1977
  authored
  145f1a8
- Publish the neuron-counts caveats instead of draft notes
  Robbie1977
  committed
  9226dbd
- Correct NBLAST coverage claim and score interpretation
  Robbie1977
  committed
  d112044
- Say what a confidence value is; fix citations
  Robbie1977
  committed
  1ccadae
- Add dataset versions to the EM table
  Robbie1977
  committed
  9a86188
- Fix MCP client setup instructions and tool coverage
  Robbie1977
  committed
  4dcc7bd
- Fix broken link to the VFB API tutorial
  Robbie1977
  committed
  1f0f504
- Fix typo
  Robbie1977
  committed
  af84f0b
- Replace dead jefferislab bridging link with the VFB pages
  Robbie1977
  committed
  414668e
- Correct the BrainTrap link path
  Robbie1977
  committed
  f008c13
- Update moved and dead profile links
  Robbie1977
  committed
  c1e5e1d
- Remove dead and lapsed links
  Robbie1977
  committed
  e0bf028
- Point at OLS4
  Robbie1977
  committed
  1fab05e
- Replace truncated Cell URL with the DOI
  Robbie1977
  committed
  3d135a8
- Fix docs navigation, fill empty landing pages, tidy the contributor list
  Robbie1977
  committed
  dd1b167
- Advertise the term sitemap index instead of 38 hardcoded shards
  Robbie1977
  committed
  f2c3d77
- Merge pull request #429 from VirtualFlyBrain/claude/docs-structure-and-gaps
  Robbie1977
  authored
  22c3b1e
- Merge pull request #428 from VirtualFlyBrain/claude/docs-correctness-fixes
  Robbie1977
  authored
  2c4ffe9
- Merge pull request #430 from VirtualFlyBrain/claude/robots-sitemap-index
  Robbie1977
  authored
  fefea5d
- Serve the hero geometry from /hero/, not /data/
  Robbie1977
  committed
  4d0dc8f
- Make the theme declare and target the pinned Hugo 0.122.0
  Robbie1977
  committed
  24fd754
- Merge pull request #431 from VirtualFlyBrain/claude/hero-geometry-path
  Robbie1977
  authored
  4fde73a
- Sit the hero brain upright and stop dimming the legs and wings
  Robbie1977
  committed
  b9aedd0
- Merge pull request #433 from VirtualFlyBrain/claude/hero-brain-rotation
  Robbie1977
  authored
  b076f0f
Commits on Aug 16, 2026
Commits on Aug 17, 2026
- Add a page of published work citing VFB
  Robbie1977
  committed
  28c587d
- Style the 404 page and rewrite its copy
  Robbie1977
  committed
  952e08a
- Send 404 visitors to the 3D browser, not the site search
  Robbie1977
  committed
  f6ca75d
- Merge pull request #441 from VirtualFlyBrain/fix/404-layout-and-copy
  Robbie1977
  authored
  dcdf1e3
Commits on Aug 18, 2026
Commits on Aug 19, 2026
Commits on Aug 20, 2026
Commits on Aug 25, 2026
- List the VFB MCP server on the APIs index page
  Robbie1977
  committed
  fe6ee6f
- more mcp documentation
  Clare72
  committed
  b2f0bca
- Merge pull request #454 from VirtualFlyBrain/docs/mcp-in-apis-index
  Robbie1977
  authored
  7a76d36
Commits on Aug 26, 2026
- Revise NeuroFly 2026 participation details
  Robbie1977
  authored
  e595c0b
Commits on Aug 28, 2026
Commits on Aug 29, 2026
- Surface dataset caveats and the machine-readable instance list
  Robbie1977
  committed
  6c1faec
- Merge pull request #460 from VirtualFlyBrain/feature/catmaid-public-anon-token
  Robbie1977
  authored
  2f96669
Commits on Aug 30, 2026
Commits on Aug 31, 2026
Commits on Sep 2, 2026
Commits on Sep 3, 2026
- Add an official VFB logo mark and modern favicons
  claude
  committed
  c49a0e6
- Merge pull request #470 from VirtualFlyBrain/feat/official-logo-favicons
  Robbie1977
  authored
  325a96c
Commits on Sep 4, 2026
- Updating contributions from GitHub
  jenkins
  committed
  9ed41cf
Commits on Sep 5, 2026
Commits on Sep 6, 2026
Commits on Sep 7, 2026
Commits on Sep 9, 2026
- adding mthods
  admclachlan
  committed
  bbc9db0
- Add CMTK install page, link to it from registration/bridging docs
  claude
  committed
  4add7f7
- Give macOS readers a no-root CMTK install script
  claude
  committed
  9fa1d6b
- Merge pull request #493 from VirtualFlyBrain/docs/cmtk-install-page
  Robbie1977
  authored
  2b2774a
- Add a Tools section with quick starts for the analysis toolchain
  claude
  committed
  cf4625a
- Add an elastix page for the FANC and BANC transforms
  claude
  committed
  50ba87e
- Merge pull request #494 from VirtualFlyBrain/docs/tools-section
  Robbie1977
  authored
  0c9725d
Commits on Sep 10, 2026

Commits

Commits on Jul 27, 2026

Commits on Aug 4, 2026

Commits on Aug 5, 2026

Commits on Aug 11, 2026

Commits on Aug 12, 2026

Commits on Aug 14, 2026

Commits on Aug 15, 2026

Commits on Aug 16, 2026

Commits on Aug 17, 2026

Commits on Aug 18, 2026

Commits on Aug 19, 2026

Commits on Aug 20, 2026