Prepare TIFF inputs

For	Users exporting scanner images to TumorQuantAI's portable layout
Hands-on steps	Export L0/L2, preserve provenance, inspect the folder
Prerequisites	Access to the scanner/export system and authoritative physical-scale metadata
Download/storage	None; exported L0 can be much larger than its source container
Writes to	A user-selected slide input directory; inspection writes a separate manifest

Portable layout

/data/slides/
├── case_001/
│   ├── 1_L0_rgb.tif
│   └── 1_L2_rgb.tif
└── case_002/
    ├── 1_L0_rgb.tif
    └── 1_L2_rgb.tif

L0 is the highest-resolution primary image analyzed. L2 is a lower-resolution companion needed by sampled modes and reports. Preserve the scanner/export record that establishes the source L0 MPP.

TumorQuantAI discovers *_L0_rgb.tif and *_L0_rgb.tiff by default. Avoid a broad *.tif pattern that can select thumbnails, companions, or outputs.

Inspect without the model

tumorquantai inspect /data/slides \
  --output /data/tumorquantai-inspection

Expected success is a reviewable manifest with one selected primary per sample, its companion, format/pyramid information when readable, embedded or supplied MPP, duplicate warnings, and storage estimates.

If MPP is absent or unreliable, obtain it from the imaging facility and supply --source-mpp for the main run. Do not infer MPP from an unrelated slide or treat target MPP as source MPP.

Stop and clean up

Press Ctrl+C during inspection and rerun. Inspection does not change the slide directory. Remove only its separate inspection output if unwanted; keep the source exports read-only.

Next: create a sample sheet or choose a preset.