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Organ transplantation serves as the primary therapeutic strategy for end-stage organ failures. However, allograft rejection is a common complication of organ transplantation. Histological assessment is essential for the timely detection and diagnosis of transplant rejection and remains the gold standard. Nevertheless, the traditional histochemical staining process is time-consuming, costly, and labor-intensive. Here, we present a panel of virtual staining neural networks for lung and heart transplant biopsies, which digitally convert autofluorescence microscopic images of label-free tissue sections into their brightfield histologically stained counterparts, bypassing the traditional histochemical staining process. Specifically, we virtually generated Hematoxylin and Eosin (H&E), Masson's Trichrome (MT), and Elastic Verhoeff-Van Gieson (EVG) stains for label-free transplant lung tissue, along with H&E and MT stains for label-free transplant heart tissue. Subsequent blind evaluations conducted by three board-certified pathologists have confirmed that the virtual staining networks consistently produce high-quality histology images with high color uniformity, closely resembling their well-stained histochemical counterparts across various tissue features. The use of virtually stained images for the evaluation of transplant biopsies achieved comparable diagnostic outcomes to those obtained via traditional histochemical staining, with a concordance rate of 82.4% for lung samples and 91.7% for heart samples. Moreover, virtual staining models create multiple stains from the same autofluorescence input, eliminating structural mismatches observed between adjacent sections stained in the traditional workflow, while also saving tissue, expert time, and staining costs., Comment: 21 Pages, 5 Figures

Histopathological staining of human tissue is essential in the diagnosis of various diseases. The recent advances in virtual tissue staining technologies using AI alleviate some of the costly and tedious steps involved in the traditional histochemical staining process, permitting multiplexed rapid staining of label-free tissue without using staining reagents, while also preserving tissue. However, potential hallucinations and artifacts in these virtually stained tissue images pose concerns, especially for the clinical utility of these approaches. Quality assessment of histology images is generally performed by human experts, which can be subjective and depends on the training level of the expert. Here, we present an autonomous quality and hallucination assessment method (termed AQuA), mainly designed for virtual tissue staining, while also being applicable to histochemical staining. AQuA achieves 99.8% accuracy when detecting acceptable and unacceptable virtually stained tissue images without access to ground truth, also presenting an agreement of 98.5% with the manual assessments made by board-certified pathologists. Besides, AQuA achieves super-human performance in identifying realistic-looking, virtually stained hallucinatory images that would normally mislead human diagnosticians by deceiving them into diagnosing patients that never existed. We further demonstrate the wide adaptability of AQuA across various virtually and histochemically stained tissue images and showcase its strong external generalization to detect unseen hallucination patterns of virtual staining network models as well as artifacts observed in the traditional histochemical staining workflow. This framework creates new opportunities to enhance the reliability of virtual staining and will provide quality assurance for various image generation and transformation tasks in digital pathology and computational imaging., Comment: 37 Pages, 7 Figures

Systemic amyloidosis is a group of diseases characterized by the deposition of misfolded proteins in various organs and tissues, leading to progressive organ dysfunction and failure. Congo red stain is the gold standard chemical stain for the visualization of amyloid deposits in tissue sections, as it forms complexes with the misfolded proteins and shows a birefringence pattern under polarized light microscopy. However, Congo red staining is tedious and costly to perform, and prone to false diagnoses due to variations in the amount of amyloid, staining quality and expert interpretation through manual examination of tissue under a polarization microscope. Here, we report the first demonstration of virtual birefringence imaging and virtual Congo red staining of label-free human tissue to show that a single trained neural network can rapidly transform autofluorescence images of label-free tissue sections into brightfield and polarized light microscopy equivalent images, matching the histochemically stained versions of the same samples. We demonstrate the efficacy of our method with blind testing and pathologist evaluations on cardiac tissue where the virtually stained images agreed well with the histochemically stained ground truth images. Our virtually stained polarization and brightfield images highlight amyloid birefringence patterns in a consistent, reproducible manner while mitigating diagnostic challenges due to variations in the quality of chemical staining and manual imaging processes as part of the clinical workflow., Comment: 20 Pages, 5 Figures

Histological examination is a crucial step in an autopsy; however, the traditional histochemical staining of post-mortem samples faces multiple challenges, including the inferior staining quality due to autolysis caused by delayed fixation of cadaver tissue, as well as the resource-intensive nature of chemical staining procedures covering large tissue areas, which demand substantial labor, cost, and time. These challenges can become more pronounced during global health crises when the availability of histopathology services is limited, resulting in further delays in tissue fixation and more severe staining artifacts. Here, we report the first demonstration of virtual staining of autopsy tissue and show that a trained neural network can rapidly transform autofluorescence images of label-free autopsy tissue sections into brightfield equivalent images that match hematoxylin and eosin (H&E) stained versions of the same samples, eliminating autolysis-induced severe staining artifacts inherent in traditional histochemical staining of autopsied tissue. Our virtual H&E model was trained using >0.7 TB of image data and a data-efficient collaboration scheme that integrates the virtual staining network with an image registration network. The trained model effectively accentuated nuclear, cytoplasmic and extracellular features in new autopsy tissue samples that experienced severe autolysis, such as COVID-19 samples never seen before, where the traditional histochemical staining failed to provide consistent staining quality. This virtual autopsy staining technique can also be extended to necrotic tissue, and can rapidly and cost-effectively generate artifact-free H&E stains despite severe autolysis and cell death, also reducing labor, cost and infrastructure requirements associated with the standard histochemical staining., Comment: 24 Pages, 7 Figures