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Biology subjects

LeBoeuf, M.

Publications and source records attributed to LeBoeuf, M..

2 recordsLinked to original sources

DeltaAI: Semi-Autonomous Tissue Grossing Measurements and Recommendations using Neural Radiance Fields for Rapid, Complete Intraoperative Histological Assessment of Tumor Margins

Mohs Micrographic Surgery (MMS) aims to excise cutaneous cancer with real-time margin analysis. However, manual tissue grossing and analysis can be inefficient, so we propose DeltaAI, a novel workflow that utilizes Neural Radiance Fields (NeRF) to enable rapid tissue grossing and generate a 3D model in an augmented reality (AR) environment. In our study, we captured 30-second videos of 17 MMS specimens using a photogrammetry turntable and cellphone camera. Preprocessing the tissues with segmentation models, we created a dataset of 923, 360-degree-view, images per video (17 videos). Using COLMAP, we estimated poses for sparse tissue reconstructions and trained the NeRF model for 3D volumetric tissue renderings. The results demonstrated that DeltaAI generated more accurate and complete 360-degree, 3D tissue renderings compared to previous models, while also achieving significantly faster runtimes. Our proposed semi-autonomous NeRF-based workflow has the potential to enhance the speed of MMS specimen processing, measurement, report generation, and margin assessment. It can inform real-time grossing decisions, automate the export of electronic health record data, and facilitate time-efficient and complete cancer excisions. Moreover, DeltaAI can contribute to the wider adoption of AI technology in clinical settings by improving tissue modeling for manual grossing.

pathology↗

Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining

The advent of spatial transcriptomics technologies has heralded a renaissance in research to advance our understanding of the spatial cellular and transcriptional heterogeneity within tissues. Spatial transcriptomics allows investigation of the interplay between cells, molecular pathways and the surrounding tissue architecture and can help elucidate developmental trajectories, disease pathogenesis, and various niches in the tumor microenvironment. Photoaging is the histological and molecular skin damage resulting from chronic/acute sun exposure and is a major risk factor for skin cancer. Spatial transcriptomics technologies hold promise for improving the reliability of evaluating photoaging and developing new therapeutics. Current challenges, including limited focus on dermal elastosis variations and reliance on self-reported measures, can introduce subjectivity and inconsistency. Spatial transcriptomics offer an opportunity to assess photoaging objectively and reproducibly in studies of carcinogenesis and discern the effectiveness of therapies that intervene on photoaging and prevent cancer. Evaluation of distinct histological architectures using highly-multiplexed spatial technologies can identify specific cell lineages that have been understudied due to their location beyond the depth of UV penetration. However, the cost and inter-patient variability using state-of-the-art assays such as the 10x Genomics Spatial Transcriptomics assays limits the scope and scale of large-scale molecular epidemiologic studies. Here, we investigate the inference of spatial transcriptomics information from routine hematoxylin and eosin-stained (H&E) tissue slides. We employed the Visium CytAssist spatial transcriptomics assay to analyze over 18,000 genes at a 50-micron resolution for four patients from a cohort of 261 skin specimens collected adjacent to surgical resection sites for basal and squamous keratinocyte tumors. The spatial transcriptomics data was co-registered with 40x resolution whole slide imaging (WSI) information. We developed machine learning models that achieved a macro-averaged median AUC and F1 score of 0.80 and 0.61 and Spearman coefficient of 0.60 in inferring transcriptomic profiles across the slides, and accurately captured biological pathways across various tissue architectures.

pathology↗