Related papers: SPAC: A Python Package for Spatial Single-Cell Ana…
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…
As camera pixel arrays have grown larger and faster, and optical microscopy techniques ever more refined, there has been an explosion in the quantity of data acquired during routine light microcopy. At the single-molecule level, analysis…
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by…
Whole slide images, with their gigapixel-scale panoramas of tissue samples, are pivotal for precise disease diagnosis. However, their analysis is hindered by immense data size and scarce annotations. Existing MIL methods face challenges due…
Hierarchical multiplex imaging approaches generate spatially resolved single-cell measurements across multiple, spatially organized fields of view (FOVs) within patient tumor specimens, thereby enabling systematic investigation of how the…
Colocalization analysis aims to study complex spatial associations between bio-molecules via optical imaging techniques. However, existing colocalization analysis workflows only assess an average degree of colocalization within a certain…
Due to its specificity, fluorescence microscopy (FM) has become a quintessential imaging tool in cell biology. However, photobleaching, phototoxicity, and related artifacts continue to limit FM's utility. Recently, it has been shown that…
The existing barely-supervised medical image segmentation (BSS) methods, adopting a registration-segmentation paradigm, aim to learn from data with very few annotations to mitigate the extreme label scarcity problem. However, this paradigm…
Fluorescence microscopy and derived techniques are continuously looking for photodetectors able to guarantee increased sensitivity, high spatial and temporal resolution and ease of integration into modern microscopy architectures. Recent…
In the era of large time-domain spectro-photometric surveys, surface variations such as starspots, chemical inhomogeneities, pulsations, rotational distortions, and binary interactions can now be directly detected and modelled. Accurately…
The tumor microenvironment (TME) is a spatially heterogeneous ecosystem where cellular interactions shape tumor progression and response to therapy. Multiplexed imaging technologies enable high-resolution spatial characterization of the…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Quantitative characterization of cellular spatial organization is critical for understanding tumor progression and immune response. Recent advances in artificial intelligence (AI) enable large-scale segmentation and classification of nuclei…
An improved analysis for single particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the AMO instrument at the Linac Coherent Light Source (LCLS) as…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…
We present SPUX - a modular framework for Bayesian inference enabling uncertainty quantification and propagation in linear and nonlinear, deterministic and stochastic models, and supporting Bayesian model selection. SPUX can be coupled to…
Time-resolved single photon imaging is a promising imaging modality characterized by the unique capability of timestamping the arrivals of single photons. Single-Photon Avalanche Diodes (SPADs) are the leading technology for implementing…
The Linac Coherent Light Source (LCLS) is an X- ray free electron laser (XFEL) facility enabling the study of the structure and dynamics of single macromolecules. A major upgrade will bring the repetition rate of the X-ray source from 120…
Advanced microscopy techniques are essential in biomedical research for visualising and tracking biomolecules within living cells and their compartments. Conventional fluorescence microscopy methods, however, often struggle with accurately…