An End-to-End Platform for Digital Pathology Using Hyperspectral Autofluorescence Microscopy and Deep Learning-Based Virtual Histology.

Conventional histopathology involves expensive and labor-intensive processes that often consume tissue samples, rendering them unavailable for other analyses. We present a novel end-to-end workflow for pathology powered by hyperspectral microscopy and deep learning. First, we developed a custom hyperspectral microscope to nondestructively image the autofluorescence of unstained tissue sections. We then trained a deep learning model to use autofluorescence to generate virtual histologic stains, which avoids the cost and variability of chemical staining procedures and conserves tissue samples. We showed that the virtual images reproduce the histologic features present in the real-stained images using a randomized nonalcoholic steatohepatitis (NASH) scoring comparison study, where both real and virtual stains are scored by pathologists (D.T., A.D.B., R.K.P.). The test showed moderate-to-good concordance between pathologists' scoring on corresponding real and virtual stains. Finally, we developed deep learning-based models for automated NASH Clinical Research Network score prediction. We showed that the end-to-end automated pathology platform is comparable with an independent panel of pathologists for NASH Clinical Research Network scoring when evaluated against the expert pathologist consensus scores. This study provides proof of concept for this virtual staining strategy, which could improve cost, efficiency, and reliability in pathology and enable novel approaches to spatial biology research.

Clinical-Grade Validation of an Autofluorescence Virtual Staining System with Human Experts and a Deep Learning System for Prostate Cancer.

The tissue diagnosis of adenocarcinoma and intraductal carcinoma of the prostate (IDC-P) includes Gleason grading of tumor morphology on the hematoxylin and eosin (H&E) stain, and immunohistochemistry (IHC) markers on the PIN-4 stain (CK5/6, P63, AMACR). In this work, we create an automated system for producing both virtual H&E and PIN-4 IHC stains from unstained prostate tissue using a high-throughput hyperspectral fluorescence microscope and artificial intelligence & machine learning. We demonstrate that the virtual stainer models can produce high-quality images suitable for diagnosis by genitourinary pathologists. Specifically, we validate our system through extensive human review and computational analysis, using a previously-validated Gleason scoring model, and an expert panel, on a large dataset of test slides. This study extends our previous work on virtual staining from autofluorescence, demonstrates the clinical utility of this technology for prostate cancer, and exemplifies a rigorous standard of qualitative and quantitative evaluation for digital pathology.