Related papers: acia-workflows: Automated Single-cell Imaging Anal…
While optical microscopy inspection of blood films and bone marrow aspirates by a hematologist is a crucial step in establishing diagnosis of acute leukemia, especially in low-resource settings where other diagnostic modalities might not be…
For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…
Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on…
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…
Image-based modeling is essential for understanding cardiovascular hemodynamics and advancing the diagnosis and treatment of cardiovascular diseases. Constructing patient-specific vascular models remains labor-intensive, error-prone, and…
Cell tracking is an essential tool in live-cell imaging to determine single-cell features, such as division patterns or elongation rates. Unlike in common multiple object tracking, in microbial live-cell experiments cells are growing,…
While many researchers use Large Language Models (LLMs) through chat-based access, their real potential lies in leveraging LLMs via application programming interfaces (APIs). This paper conceptualizes LLMs as universal text processing…
Understanding cell cycle dynamics is crucial for studying biological processes such as growth, development and disease progression. While fluorescent protein reporters like the Fucci system allow live monitoring of cell cycle phases, they…
Purpose: In this work, we present a collaboration to create a validation dataset of pathologist annotations for algorithms that process whole slide images (WSIs). We focus on data collection and evaluation of algorithm performance in the…
Whole slide imaging (WSI) has moved digital pathology closer to diagnostic practice in recent years. Due to the inherent tissue topography variability, accurate autofocusing remains a critical challenge for WSI and automated microscopy…
Despite advancements in robotic-assisted surgery, automating complex tasks like suturing remain challenging due to the need for adaptability and precision. Learning-based approaches, particularly reinforcement learning (RL) and imitation…
Pathologists are facing an increasing workload due to a growing volume of cases and the need for more comprehensive diagnoses. Aiming to facilitate workload reduction and faster turnaround times, we developed an artificial intelligence (AI)…
Time-lapse fluorescent microscopy (TLFM) combined with predictive mathematical modelling is a powerful tool to study the inherently dynamic processes of life on the single-cell level. Such experiments are costly, complex and labour…
Biomedical imaging and RNA sequencing with single-cell resolution improves our understanding of white blood cell diseases like leukemia. By combining morphological and transcriptomic data, we can gain insights into cellular functions and…
Whole-slide image (WSI) preprocessing, comprising tissue detection followed by patch extraction, is foundational to AI-driven computational pathology but remains a major bottleneck for scaling to large and heterogeneous cohorts. We present…
The scarcity of annotated surgical data poses a significant challenge for developing deep learning systems in computer-assisted interventions. While diffusion models can synthesize realistic images, they often suffer from data memorization,…
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…
From climate science to drug discovery, scientific computing demands have surged dramatically in recent years -- driven by larger datasets, more sophisticated models, and higher simulation fidelity. This growth rate far outpaces transistor…
AtomAI is an open-source software package bridging instrument-specific Python libraries, deep learning, and simulation tools into a single ecosystem. AtomAI allows direct applications of the deep convolutional neural networks for atomic and…
Analysis of microscopy images is one important tool in many fields of biomedical research, as it allows the quantification of a multitude of parameters at the cellular level. However, manual counting of these images is both tiring and…