Skip to content
Permalink

Comparing changes

Choose two branches to see what’s changed or to start a new pull request. If you need to, you can also or learn more about diff comparisons.

Open a pull request

Create a new pull request by comparing changes across two branches. If you need to, you can also . Learn more about diff comparisons here.
base repository: Genentech/SpatialAgent
Failed to load repositories. Confirm that selected base ref is valid, then try again.
Loading
base: main
Choose a base ref
...
head repository: Genentech/SpatialAgent
Failed to load repositories. Confirm that selected head ref is valid, then try again.
Loading
compare: case
Choose a head ref
Checking mergeability… Don’t worry, you can still create the pull request.
  • 5 commits
  • 66 files changed
  • 3 contributors

Commits on Feb 17, 2026

  1. Add demo notebooks for case studies 

    Includes annotation, cell-cell communication, panel design, and
subagent demo notebooks with example outputs.
    @hansen7
    hansen7 committed Feb 17, 2026
    Configuration menu
    Copy the full SHA
    4ccc107 View commit details
    Browse the repository at this point in the history

Commits on Feb 23, 2026

  1. Add Visium cell type annotation demo notebook with executed outputs

    @yichunher
    yichunher committed Feb 23, 2026
    Configuration menu
    Copy the full SHA
    ac1c20f View commit details
    Browse the repository at this point in the history

Commits on Apr 13, 2026

  1. Add case study demos: tonsil CosMx and colitis MERFISH 

    - case_tonsil_cosmx: healthy human tonsil CosMx (Fig5) — neighborhood,
  trajectory, and gene imputation analyses with notebooks, figures, and reports
- case_colitis_merfish: mouse DSS colitis MERFISH progression (Fig6) —
  cell-neighborhood, CCC, and trajectory analyses
- case_study_dataset_harmonization.ipynb and case_study_spatial_grn.ipynb
- Large notebooks and PNGs tracked via Git LFS

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
    @hansen7 @claude
    hansen7 and claude committed Apr 13, 2026
    Configuration menu
    Copy the full SHA
    39b4d2d View commit details
    Browse the repository at this point in the history

Commits on May 4, 2026

  1. Merge branch 'main' of github.com:Genentech/SpatialAgent into case

    @hansen7
    hansen7 committed May 4, 2026
    Configuration menu
    Copy the full SHA
    0578c6e View commit details
    Browse the repository at this point in the history

  2. Trim demo notebooks and refresh notebooks README 

    Remove cadinu_v6-hc, cadinu_subagent_demo, and cell_cell_communication
notebooks (superseded by the case studies in case_tonsil_cosmx and
case_colitis_merfish). Update notebooks/README.md file tree to reflect
the current structure.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
    @hansen7 @claude
    hansen7 and claude committed May 4, 2026
    Configuration menu
    Copy the full SHA
    a368ecb View commit details
    Browse the repository at this point in the history
Loading