Related papers: Whole slide and microscopy image analysis with QuP…
The field of digital pathology has seen a proliferation of deep learning models in recent years. Despite substantial progress, it remains rare for other researchers and pathologists to be able to access models published in the literature…
The integration of AI in digital pathology, particularly in whole slide image (WSI) and spatial transcriptomics (ST) analysis, holds immense potential for enhancing our understanding of diseases. Despite challenges such as training pattern…
Oblique plane microscopy, OPM, is a form of lightsheet microscopy that permits volumetric imaging of biological samples at high temporal and spatial resolution. However, the imaging geometry of OPM, and related variants of light sheet…
Backgr: Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology.…
In the rapidly evolving field of bioimaging, the integration and orchestration of Findable, Accessible, Interoperable, and Reusable (FAIR) image analysis workflows remains a challenge. We introduce BIOMERO, a bridge connecting OMERO, a…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
In many research areas, scientific progress is accelerated by multidisciplinary access to image data and their interdisciplinary annotation. However, keeping track of these annotations to ensure a high-quality multi-purpose data set is a…
Quantitative analysis of multidimensional biological images is useful for understanding complex cellular phenotypes and accelerating advances in biomedical research. As modern microscopy generates ever-larger 2D and 3D datasets, existing…
Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is…
Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source options exist for deploying models in…
Quantitative phase imaging (QPI) is a label-free computational imaging technique that provides optical path length information of specimens. In modern implementations, the quantitative phase image of an object is reconstructed digitally…
We develop an open-source, end-to-end software (named QHDOPT), which can solve nonlinear optimization problems using the quantum Hamiltonian descent (QHD) algorithm. QHDOPT offers an accessible interface and automatically maps tasks to…
In this study, we built an end-to-end tumor-infiltrating lymphocytes (TILs) assessment pipeline within QuPath, demonstrating the potential of easily accessible tools to perform complex tasks in a fully automatic fashion. First, we trained a…
Biological and biomedical imaging datasets record the constitution, architecture and dynamics of living organisms across several orders of magnitude of space and time. Imaging technologies are now used throughout the life and biomedical…
Imaging specimens over large scales and with a sub-micron resolution is instrumental to biomedical research. Yet, the number of pixels to form such an image usually exceeds the number of pixels provided by conventional cameras. While most…
Quantitative phase imaging (QPI) is a label-free computational imaging technique used in various fields, including biology and medical research. Modern QPI systems typically rely on digital processing using iterative algorithms for phase…
Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology…
Quantum Process Tomography (QPT) methods aim at identifying, i.e. estimating, a quantum process. QPT is a major quantum information processing tool, since it especially allows one to experimentally characterize the actual behavior of…
Whole-slide image analysis via the means of computational pathology often relies on processing tessellated gigapixel images with only slide-level labels available. Applying multiple instance learning-based methods or transformer models is…
Autoplot is software developed for the Virtual Observatories in Heliophysics to provide intelligent and automated plotting capabilities for many typical data products that are stored in a variety of file formats or databases. Autoplot has…