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Building on our previously introduced Multi-cell Monte Carlo (MC)^2 method for modeling phase coexistence, this paper provides important improvements for efficient determination of phase equilibria in solids. The (MC)^2 method uses multiple…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
The most realistic information about the transparent sample such as a live cell can be obtained only using bright-field light microscopy. At high-intensity pulsing LED illumination, we captured a primary 12-bit-per-channel (bpc) response…
We have developed an automatic method for segmenting fluorescence lifetime (FLT) imaging microscopy (FLIM) images of cells inspired by a multi-resolution community detection (MCD) based network segmentation method. The image processing…
The purpose of this paper is to provide an algorithm for detecting and tracking astral MTs in a fully automated way and supply a description of their dynamic behaviour. For the algorithm testing, a dataset of stacks (i.e. time-lapse image…
Digital holographic microscopy is a thriving imaging modality that attracted considerable research interest in quantitative biological cell imaging due to its ability to not only create excellent label-free contrast, but also supply…
Analyzing the dynamic changes of cellular morphology is important for understanding the various functions and characteristics of live cells, including stem cells and metastatic cancer cells. To this end, we need to track all points on the…
Global fits of physics models require efficient methods for exploring high-dimensional and/or multimodal posterior functions. We introduce a novel method for accelerating Markov Chain Monte Carlo (MCMC) sampling by pairing a…
The MiDeSeC dataset is created through H&E stained invasive breast carcinoma, no special type (NST) slides of 25 different patients captured at 40x magnification from the Department of Medical Pathology at Ankara University. The slides have…
We report DynaCLR, a self-supervised method for embedding cell and organelle Dynamics via Contrastive Learning of Representations of time-lapse images. DynaCLR integrates single-cell tracking and time-aware contrastive sampling to learn…
Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic…
Advanced image segmentation and processing tools present an opportunity to study cell processes and their dynamics. However, image analysis is often routine and time-consuming. Nowadays, alternative data-driven approaches using deep…
Solving inverse problems in natural sciences often requires a search pro- cess to find explanatory models that match collected field data. Inverse problems are often under-determined meaning that there are many poten- tial explanatory…
Cellphones equipped with high-quality cameras and powerful CPUs as well as GPUs are widespread. This opens new prospects to use such existing computational and imaging resources to perform medical diagnosis in developing countries at a very…
Manual operation of microscopes for repetitive tasks in cell biology is a significant bottleneck, consuming invaluable expert time, and introducing human error. Automation is essential, and while Digital Holographic Microscopy (DHM) offers…
3D fluorescence microscopy of living organisms has increasingly become an essential and powerful tool in biomedical research and diagnosis. An exploding amount of imaging data has been collected, whereas efficient and effective…
Pathology images of histopathology can be acquired from camera-mounted microscopes or whole slide scanners. Utilizing similarity calculations to match patients based on these images holds significant potential in research and clinical…
In addition to the optical aberrations, the magnitude of the optical cells of detectors is one of the most important parameters, which restricts the resolution of detectors. Adaptive optic and the methods of reducing the aberrations are…
T cells use sophisticated shape dynamics (morphodynamics) to migrate towards and neutralise infected and cancerous cells. However, there is limited quantitative understanding of the migration process in 3D extracellular matrices (ECMs) and…
Inspection of tissues using a light microscope is the primary method of diagnosing many diseases, notably cancer. Highly multiplexed tissue imaging builds on this foundation, enabling the collection of up to 60 channels of molecular…