Related papers: Multimarginal Wasserstein Barycenter for Stain Nor…
Purpose: In digital histopathology, virtual multi-staining is important for diagnosis and biomarker research. Additionally, it provides accurate ground-truth for various deep-learning tasks. Virtual multi-staining can be obtained using…
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…
Image registration refers to the process of spatially aligning two or more images by mapping them into a common coordinate system, so that corresponding anatomical or tissue structures are matched across images. In digital pathology,…
Variability in staining protocols, such as different slide preparation techniques, chemicals, and scanner configurations, can result in a diverse set of whole slide images (WSIs). This distribution shift can negatively impact the…
The analysis of FFPE tissue sections stained with haematoxylin and eosin (H&E) or immunohistochemistry (IHC) is an essential part of the pathologic assessment of surgically resected breast cancer specimens. IHC staining has been broadly…
Stain normalization algorithms aim to transform the color and intensity characteristics of a source multi-gigapixel histology image to match those of a target image, mitigating inconsistencies in the appearance of stains used to highlight…
Early diagnosis of the cancer cells is necessary for making an effective treatment plan and for the health and safety of a patient. Nowadays, doctors usually use a histological grade that pathologists determine by performing a…
In this paper we propose to perform model ensembling in a multiclass or a multilabel learning setting using Wasserstein (W.) barycenters. Optimal transport metrics, such as the Wasserstein distance, allow incorporating semantic side…
Deploying deep learning-based imaging tools across various clinical sites poses significant challenges due to inherent domain shifts and regulatory hurdles associated with site-specific fine-tuning. For histopathology, stain normalization…
Wasserstein Barycenter is a principled approach to represent the weighted mean of a given set of probability distributions, utilizing the geometry induced by optimal transport. In this work, we present a novel scalable algorithm to…
The popular use of histopathology images, such as hematoxylin and eosin (H&E), has proven to be useful in detecting tumors. However, moving such cancer cases forward for treatment requires accurate on the amount of the human epidermal…
Immunohistochemical (IHC) staining highlights the molecular information critical to diagnostics in tissue samples. However, compared to H&E staining, IHC staining can be much more expensive in terms of both labor and the laboratory…
Hyperspectral unmixing is a blind source separation problem which consists in estimating the reference spectral signatures contained in a hyperspectral image, as well as their relative contribution to each pixel according to a given mixture…
Optimal transport is a notoriously difficult problem to solve numerically, with current approaches often remaining intractable for very large scale applications such as those encountered in machine learning. Wasserstein barycenters -- the…
While human observers are able to cope with variations in color and appearance of histological stains, digital pathology algorithms commonly require a well-normalized setting to achieve peak performance, especially when a limited amount of…
In histology, the presence of collagen in the extra-cellular matrix has both diagnostic and prognostic value for cancer malignancy, and can be highlighted by adding Saffron (S) to a routine Hematoxylin and Eosin (HE) staining. However,…
We present new algorithms to compute the mean of a set of empirical probability measures under the optimal transport metric. This mean, known as the Wasserstein barycenter, is the measure that minimizes the sum of its Wasserstein distances…
Due to its superior efficiency in utilizing annotations and addressing gigapixel-sized images, multiple instance learning (MIL) has shown great promise as a framework for whole slide image (WSI) classification in digital pathology…
Spatial Transcriptomics (ST) allows a high-resolution measurement of RNA sequence abundance by systematically connecting cell morphology depicted in Hematoxylin and Eosin (H&E) stained histology images to spatially resolved gene…
Staining reveals the micro structure of the aspirate while creating histopathology slides. Stain variation, defined as a chromatic difference between the source and the target, is caused by varying characteristics during staining, resulting…