Add GrandQC slide quality control notebook for IDC DICOM WSI#105
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fedorov wants to merge 3 commits into
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Add GrandQC slide quality control notebook for IDC DICOM WSI#105fedorov wants to merge 3 commits into
fedorov wants to merge 3 commits into
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Demonstrates end-to-end use of GrandQC with NCI Imaging Data Commons: - Discover H&E slides via idc-index sm_index metadata - Patch GrandQC scripts for native DICOM directory support via OpenSlide 4.0 - Download TCGA-BRCA DICOM series and run tissue detection + artifact segmentation - Visualize results using GrandQC's own wsi_colors.py palette - Validate the DICOM-based pipeline against GrandQC's pre-computed TCGA masks (zenodo.org/records/14041578) by comparing per-class artifact fractions Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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main.py loads a fully-pickled QC model via torch.load(), which fails with exit code 1 under PyTorch >=2.6 (weights_only=True default). Patch the load to weights_only=False so the trusted Zenodo weights unpickle. Also add [i/N] progress reporting and a failure guard that records per-slide errors and exits non-zero, so the notebook surfaces failures the loop used to swallow. Add grandqc_slide_quality_resolution_notes.md documenting the model working resolution (MPP 1.5) vs. the fixed 512x512 input tile, how MPP is read from openslide.mpp-x (DICOM PixelSpacing), and an empirical confirmation on an IDC slide; link it from the Part 4 intro. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Clone the fedorov/grandqc idc-dicom-fixes branch, which carries the DICOM-directory, device-detection, PyTorch >=2.6 load, small-slide overlay, and fail-loud fixes as proper commits. Replace the in-notebook patch_grandqc_for_dicom() cell with a verification cell that asserts the fixes are present in the cloned scripts, and update Part 2 prose plus the resolution notes accordingly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Demonstrates end-to-end use of GrandQC with NCI Imaging Data Commons: