Related papers: Whole slide and microscopy image analysis with QuP…
The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…
Quantitative phase imaging (QPI) has been widely applied in characterizing cells and tissues. Spatial light interference microscopy (SLIM) is a highly sensitive QPI method, due to its partially coherent illumination and common path…
Pathology is essential for cancer diagnosis, with multiple instance learning (MIL) widely used for whole slide image (WSI) analysis. WSIs exhibit a natural hierarchy -- patches, regions, and slides -- with distinct semantic associations.…
Running a quantum circuit on current hardware involves a sequence of engineering decisions, each with tunable parameters and distinct error characteristics. Existing tools optimize each decision in isolation, leaving practitioners unable to…
Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem…
Conventional histopathology has long been essential for disease diagnosis, relying on visual inspection of tissue sections. Immunohistochemistry aids in detecting specific biomarkers but is limited by its single-marker approach, restricting…
Whole slide images (WSIs) pose unique challenges when training deep learning models. They are very large which makes it necessary to break each image down into smaller patches for analysis, image features have to be extracted at multiple…
Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables to simulate operational light-sheet microscopes by combining data…
Spatial cluster analysis (SCA) offers valuable insights into biological images; a common SCA technique is sliding window analysis (SWA). Unfortunately, SWA's computational cost hinders its application to larger images, limiting its use to…
Distributed, large-scale quantum computing will need architectures that combine matter-based qubits with photonic links, but today's software stacks target either gate-based chips or linear-optical devices in isolation. We introduce Optyx,…
We present Qibolab, an open-source software library for quantum hardware control integrated with the Qibo quantum computing middleware framework. Qibolab provides the software layer required to automatically execute circuit-based algorithms…
We report the development of a scalar quantization approach that helps build tables of decision and reconstruction levels for any probability density function (pdf). Several example pdf's are used for illustration: Uniform, Gaussian,…
Whole Slide Image (WSI) analysis, with its ability to reveal detailed tissue structures in magnified views, plays a crucial role in cancer diagnosis and prognosis. Due to their giga-sized nature, WSIs require substantial storage and…
In recent years, "U-shaped" neural networks featuring encoder and decoder structures have gained popularity in the field of medical image segmentation. Various variants of this model have been developed. Nevertheless, the evaluation of…
Haplotype phasing, the process of resolving parental allele inheritance patterns in diploid genomes, is critical for precision medicine and population genetics, yet the underlying optimization is NP-hard, posing a scalability challenge. To…
Advanced Hyperspectral Data Analysis Software (AVHYAS) plugin is a python3 based quantum GIS (QGIS) plugin designed to process and analyse hyperspectral (Hx) images. It is developed to guarantee full usage of present and future Hx airborne…
In this paper, a novel method of quantum image rotation (QIR) based on shear transformations on NEQR quantum images is proposed. To compute the horizontal and vertical shear mappings required for rotation, we have designed quantum…
We present QUBODock, a pip-installable tool that formulates ligand pose generation as a Quadratic Unconstrained Binary Optimization (QUBO) problem and solves it efficiently on CPU or GPU. QUBODock focuses exclusively on pose generation and…
Weak supervision learning on classification labels has demonstrated high performance in various tasks, while a few pixel-level fine annotations are also affordable. Naturally a question comes to us that whether the combination of…
PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0):…