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Weakly Supervised AI for Efficient Analysis of 3D Pathology Samples
Jul 27, 2023
Human tissue and its constituent cells form a microenvironment that is fundamentally three-dimensional (3D). However, the standard-of-care in pathologic diagnosis involves selecting a few two-dimensional (2D) sections for microscopic evaluation, risking sampling bias and misdiagnosis. Diverse methods for capturing 3D tissue morphologies have been developed, but they have yet had little translation to clinical practice; manual and computational evaluations of such large 3D data have so far been impractical and/or unable to provide patient-level clinical insights. Here we present Modality-Agnostic Multiple instance learning for volumetric Block Analysis (MAMBA), a deep-learning-based platform for processing 3D tissue images from diverse imaging modalities and predicting patient outcomes. Archived prostate cancer specimens were imaged with open-top light-sheet microscopy or microcomputed tomography and the resulting 3D datasets were used to train risk-stratification networks based on 5-year biochemical recurrence outcomes via MAMBA. With the 3D block-based approach, MAMBA achieves an area under the receiver operating characteristic curve (AUC) of 0.86 and 0.74, superior to 2D traditional single-slice-based prognostication (AUC of 0.79 and 0.57), suggesting superior prognostication with 3D morphological features. Further analyses reveal that the incorporation of greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, suggesting the value of capturing larger extents of heterogeneous 3D morphology. With the rapid growth and adoption of 3D spatial biology and pathology techniques by researchers and clinicians, MAMBA provides a general and efficient framework for 3D weakly supervised learning for clinical decision support and can help to reveal novel 3D morphological biomarkers for prognosis and therapeutic response.
Aging display's effect on interpretation of digital pathology slides
Jun 30, 2015It is our conjecture that the variability of colors in a pathology image effects the interpretation of pathology cases, whether it is diagnostic accuracy, diagnostic confidence, or workflow efficiency. In this paper, digital pathology images are analyzed to quantify the perceived difference in color that occurs due to display aging, in particular a change in the maximum luminance, white point, and color gamut. The digital pathology images studied include diagnostically important features, such as the conspicuity of nuclei. Three different display aging models are applied to images: aging of luminance & chrominance, aging of chrominance only, and a stabilized luminance & chrominance (i.e., no aging). These display models and images are then used to compare conspicuity of nuclei using CIE deltaE2000, a perceptual color difference metric. The effect of display aging using these display models and images is further analyzed through a human reader study designed to quantify the effects from a clinical perspective. Results from our reader study indicate significant impact of aged displays on workflow as well as diagnosis as follow. As compared to the originals (no-aging), slides with the effect of aging simulated were significantly more difficult to read (p-value of 0.0005) and took longer to score (p-value of 0.02). Moreover, luminance+chrominance aging significantly reduced inter-session percent agreement of diagnostic scores (p-value of 0.0418).