ArticleJournal of biomedical optics2021
Quantifying the effects of biopsy fixation and staining panel design on automatic instance segmentation of immune cells in human lupus nephritis.
Article in Journal of biomedical optics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Pseudo-spectral angle mapping for pixel and cell classification in highly multiplexed immunofluorescence images.Journal of medical imaging (Bellingham, Wash.) · 2024Article
- Pseudo-spectral angle mapping for automated pixel-level analysis of highly multiplexed tissue image data.bioRxiv : the preprint server for biology · 2024Article
- Specific in situ inflammatory states associate with progression to renal failure in lupus nephritis.The Journal of clinical investigation · 2022Article
- Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images.The American journal of pathology · 2021Review
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6 authors.
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Abstract
significanceLupus nephritis (LuN) is a chronic inflammatory kidney disease. The cellular mechanisms by which LuN progresses to kidney failure are poorly characterized. Automated instance segmentation of immune cells in immunofluorescence images of LuN can probe these cellular interactions.
aimOur specific goal is to quantify how sample fixation and staining panel design impact automated instance segmentation and characterization of immune cells. APPROACH: Convolutional neural networks (CNNs) were trained to segment immune cells in fluorescence confocal images of LuN biopsies. Three datasets were used to probe the effects of fixation methods on cell features and the effects of one-marker versus two-marker per cell staining panels on CNN performance.
resultsNetworks trained for multi-class instance segmentation on fresh-frozen and formalin-fixed, paraffin-embedded (FFPE) samples stained with a two-marker panel had sensitivities of 0.87 and 0.91 and specificities of 0.82 and 0.88, respectively. Training on samples with a one-marker panel reduced sensitivity (0.72). Cell size and intercellular distances were significantly smaller in FFPE samples compared to fresh frozen (Kolmogorov-Smirnov, p ≪ 0.0001).
conclusionsFixation method significantly reduces cell size and intercellular distances in LuN biopsies. The use of two markers to identify cell subsets showed improved CNN sensitivity relative to using a single marker.
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