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Reconstructing published images

Install the OpenSlide native library and Python bindings in the PBSBench Conda environment before running the WSI commands:

conda install --channel conda-forge openslide openslide-python -y

Download and extract S-BIAD440. Its images/ directory must contain WSI files such as III_1.tiff.

pbsbench-prepare-data \
  --annotations data/PBSInstr/cell_captions.jsonl \
                data/PBSInstr/cell_train.jsonl data/PBSInstr/cell_val.jsonl \
                data/PBSInstr/slide_train.jsonl data/PBSInstr/slide_val.jsonl \
                data/PBSBench/cell_id_test.jsonl data/PBSBench/slide_id_test.jsonl \
  --source S-BIAD440=/path/to/extracted/S-BIAD440 \
  --output data/images

The annotations store the original slide filename, 512 × 512 patch origin, curated Cellpose-SAM object index, and bounding box. The command reads the region directly from the WSI and reproduces the contextual 224 × 224 cell crop used during QA curation. It also saves the corresponding patch and symlinks slide-level images. Use --link-mode copy if symlinks are unsuitable.

OOD records refer to images distributed by their source datasets. Provide one root for every source named in the selected annotations, for example:

pbsbench-prepare-data --annotations data/PBSBench/cell_ood_test.jsonl \
  --source AML-Cytomorphology_LMU=/path/to/AML-Cytomorphology_LMU \
  --source APL=/path/to/APL \
  --source WBC_LISC=/path/to/WBC_LISC \
  --output data/images

The root may be either the extracted dataset directory or a parent directory introduced by the download tool. The materializer first checks the provider-native relative path, then searches nested extraction directories by the unique source filename. It also recognizes Roboflow export names such as Baso_46-1__8_bmp.rf.<hash>.jpg for the published source locator Baso_46-1__8.bmp. Ambiguous or missing matches stop with an error rather than silently selecting an image.

Generated images are ignored by Git. The source datasets retain their own licenses.

WSI patches and Phase-2 features

After materializing the S-BIAD440 slides, create non-overlapping 512-pixel patches. Pass --qc-model to apply an available Haemorasis QC model; without it, all patches are retained.

pbsbench-tile \
  --slides data/images/slides/S-BIAD440 \
  --output data/processed/patches \
  --patch-size 512

pbsbench-extract-features \
  --config configs/02_cell_patch_alignment.yaml \
  --checkpoint checkpoints/cell_patch_alignment \
  --patches data/processed/patches \
  --output data/processed/patch_features

The extractor preserves slide names: patches under III_1/ become III_1.pt. Each file stores fixed-length Phase-2 Perceiver tokens and the ordered patch filenames. These generated files are ignored by Git.