[upgrade] Cellpose: identify current Wave-container version pin vs upstream v4.1.1

Current state

• Pinned: container community.wave.seqera.io/library/python_pip_cellpose:fdf7a8c3a305a26e at modules/nf-core/cellpose/main.nf:9
• Modules: modules/nf-core/cellpose
• Pipeline modes: image (when --method cellpose, the default)

Latest upstream

• v4.1.1 (released 2026-03-31): https://github.com/MouseLand/cellpose/releases/tag/v4.1.1
• v4.1.0 (2026-03-25), v4.0.x (Mar 2026 patch series)
• v4.x branch is the current generation (post-v3 architectural change to single-model cyto3)

Investigation needed

1. What cellpose version is fdf7a8c3a305a26e? The Wave container hash doesn't reveal the underlying pip-installed cellpose version. Need to either:
   • Decode by pulling the container and running cellpose --version
   • Look at the Wave build manifest, or
   • Trace the original Seqera Wave recipe
2. Are we on v3 or v4? v3 → v4 had architectural changes (single-model cyto3 instead of separate models). If we're on v3, this is a substantial test surface; if already v4, a minor bump.
3. Behavioral compatibility of our existing args (--flow_threshold 0, --batch_size 1) at the latest version.

Migration plan

• Decode the Wave container to determine the current cellpose version
• Review v4.1.1 changelog for behavioral changes affecting --flow_threshold / --batch_size / model selection
• If a minor bump (within v4.x), update the Wave container; if v3 → v4, plan a model-switch and re-benchmark
• Re-run image-mode tests on a Xenium v1 bundle to confirm segmentation quality matches

Risks

• v3 → v4 architectural change is a notable test surface (different default models, different argument defaults)
• GPU container variant: nf-core/cellpose may have separate CPU/GPU containers — bump consistently
• Atera relevance: image mode is touched by Atera workflow but blocked by XR (out of scope per user direction); this upgrade primarily helps Xenium v1 image mode

Cross-links

• Triggered by: Atera compatibility session 2026-05-28 (broader tool inventory check).

Start at modules/nf-core/cellpose/main.nf and inspect the pinned Wave container fdf7a8c3a305a26e. Pull the container or inspect its Wave manifest to identify the installed Cellpose version, then review v4.1.1 changes for --flow_threshold 0, --batch_size 1, and model selection. Done means determining whether this is a minor v4 bump or a v3-to-v4 migration, updating relevant containers if appropriate, and rerunning image-mode tests on a Xenium v1 bundle.