3D pathology of prostate biopsies with biochemical recurrence outcomes: raw H&E-analog datasets and image translation-assisted segmentation in 3D (ITAS3D) datasets (PCa_Bx_3Dpathology)

This collection provides public access to a 3D pathology dataset of prostate cancer, allowing researchers to further investigate various 3D tissue structures and their correlation with prostate cancer patient outcomes (biochemical recurrence). These 3D tissue structures are revealed through: (1) a H&E-analog stain, (2) synthetically generated immunofluorescence staining of CK8 (targeting the luminal epithelial cells of all prostate glands), and (3) 3D segmentation masks of the gland lumen, epithelium, and stromal regions of prostate biopsies. This data collection will promote research in the field of computational 3D pathology for clinical decision support. In this TCIA collection, we provide the raw 3D open-top light-sheet (OTLS) microscope images of prostate biopsies stained with a fluorescent analog of H&E at original resolution (unfused image tiles), the 2x down-sampled fused OTLS-imaged images (H&E-analog staining), the synthetic cytokeratin-8 (CK8) immunofluorescent images at 2x-downsampled resolution, the 3D semantic segmentation masks of glands at 4x down-sampled resolution, the clinical data for patient outcomes (biochemical recurrence), and the coordinates for the cancer-enriched regions of each biopsy. All datasets are from the 50 patient cases studied in this publication: [W. Xie et al., Cancer Research, 2022]. Note that the 3D pathology datasets provided in this collection were generated in Dr. Jonathan Liu’s lab at the University of Washington with a custom open-top light-sheet (OTLS) microscope developed by the lab [A.K. Glaser et al., Nature Communications, 2019]. There is no clinical metadata within the imaging files and all patients are referred to with coded identifiers. All of the clinical outcomes data provided in this collection have already been published within the supplement of [W. Xie et al., Cancer Research, 2022].