Multi Project Batch Isolation

Multi-Project Batch Signal Isolation

Experiment Overview

Context

Only 1 of ~20 registered projects (CX_19-001_SP_CC2-A28) had completed signal isolation. That project had 26 hand-tuned legacy recipes and its outcomes were recorded to the parameter learning DB. The remaining projects needed AF subtraction but had no project-specific recipes. A single-project kintsugi workflow isolate run command existed but couldn't orchestrate multiple projects or source parameters from across datasets.

Key challenge: Not all markers have recipes in every project. Need a cascading fallback system that uses the best available source per marker.

Verified Workflow

CLI Commands

# Preview all eligible projects and recipe sources
kintsugi workflow isolate batch /path/to/KINTSUGI_Projects --dry-run

# Process single project (test before full batch)
kintsugi workflow isolate batch . -d CX_19-003_spleen_CC1-A

# Full batch with learning enabled
kintsugi workflow isolate batch /blue/maigan/smith6jt/KINTSUGI_Projects --learn

# Force reprocess + custom template
kintsugi workflow isolate batch . -f --template-recipe-dir /path/to/recipes

Cascading Recipe Resolution (4 tiers)

Tissue Type Parsing (regex, case-insensitive)

_TISSUE_PATTERNS = [
    (r"(?:_SP_|spleen|splenic)", "spleen"),
    (r"(?:_LN_|lymph.?node|lymph)", "lymph_node"),
    (r"(?:_TH_|thymus|thymic)", "thymus"),
    (r"(?:pancrea)", "pancreas"),
]

Fallback: experiment.json name field, then "unknown".

Architecture: Two-Pass Processing

Markers with recipes (tiers 1-3) use _write_recipes_as_param_files() to serialize resolved recipes into temp param files, then call process_batch(recipe_dir=tmpdir). Markers without recipes (tier 4) call process_batch() without recipe_dir for auto-analysis. Results are merged into a single signal_isolation_manifest.json.

Failed Attempts (Critical)

Final Parameters

# Discovery
config_path = project / "workflow" / "config.yaml"  # Must exist
registered_dir = project / "data" / "processed" / "registered"  # Must have .tif files
manifest_path = ".../signal_isolated/signal_isolation_manifest.json"  # Skip if exists

# Recipe search dirs (in order)
_RECIPE_SEARCH_DIRS = [
    "data/processed/Processing_parameters",
    "Processing_parameters",
    "notebooks/Processing_parameters",
]

# Default template project
DEFAULT_TEMPLATE_PROJECT = "CX_19-001_SP_CC2-A28"

# Learning DB confidence threshold
min_confidence = 0.6

# Processing defaults
tile_smooth_sigma = 0.0  # No blank smoothing (recipes don't need it)
method = "auto"  # Per-marker: global vs weighted
learn = True  # Record outcomes for cross-dataset transfer

Key Insights

• 17 of ~48 project directories are eligible (have config.yaml + registered images, no existing manifest)
• Most markers resolve from learned DB (CX_19-001 spleen params cover ~18/28 markers per spleen project)
• Lymph node projects fall through to template for 2-4 markers not in the spleen learning DB
• _write_recipes_as_param_files() roundtrips cleanly — load_legacy_recipes() can read the generated files
• recipe_source field on ChannelResult tracks provenance ("own_recipe", "learned", "template", "auto")
• Sequential processing is correct for shared filesystem — parallel would cause I/O contention
• Error isolation per project — one project failure doesn't stop the batch
• Cross-project report batch_isolation_report_{timestamp}.json saved to projects_dir

Key Files

• src/kintsugi/signal/batch_multi.py — Core: discovery, tissue parsing, recipe resolution, orchestration
• src/kintsugi/signal/batch.py — Single-project processing, ChannelResult.recipe_source field
• src/kintsugi/cli.py — @isolate_group.command("batch") CLI
• tests/test_batch_multi_project.py — 34 tests (tissue parsing, discovery, resolution, roundtrip)
• src/kintsugi/signal/CLAUDE.md — Documentation

References

• Builds on batch-signal-isolation skill (single-project recipe-driven processing)
• Uses batch-orchestration-script pattern (sequential, error isolation, per-dataset filtering)
• Follows claude-md-context-management for documentation placement