Related papers: PySTACHIO: Python Single-molecule TrAcking stoiCHi…
Driven by physical questions pertaining to quantifying particle dynamics, microscopy can now resolve complex systems at the single particle level, from cellular organisms to individual ions. Yet, available analysis techniques face…
Two-dimensional electronic spectroscopy provides information on coupling and energy transfer between excited states on ultrafast timescales. Only recently, incoherent fluorescence detection has made it possible to combine this method with…
Tracking individual cells in live-cell imaging provides fundamental insights, inevitable for studying causes and consequences of phenotypic heterogeneity, responses to changing environmental conditions or stressors. Microbial cell tracking,…
Machine learning is revolutionizing image-based diagnostics in pathology and radiology. ML models have shown promising results in research settings, but their lack of interoperability has been a major barrier for clinical integration and…
The need for single-camera 3D particle tracking methods is growing, among others, due to the increasing focus in biomedical research often relying on single-plane microscopy imaging. Defocusing-based methods are ideal for a wide-spread use…
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…
Background and Objective: Deep learning enables tremendous progress in medical image analysis. One driving force of this progress are open-source frameworks like TensorFlow and PyTorch. However, these frameworks rarely address issues…
Single-cell transcriptomics techniques, such as scRNA-seq, attempt to characterize gene expression profiles in each cell of a heterogeneous sample individually. Due to growing amounts of data generated and the increasing complexity of the…
Luminescence imaging is invaluable for studying biological and material systems, particularly when advanced protocols that exploit temporal dynamics are employed. However, implementing such protocols often requires custom instrumentation,…
The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle…
The study of moving particles (e.g. molecules, virus, vesicles, organelles, or whole cells) is crucial to decipher a plethora of cellular mechanisms within physiological and pathological conditions. Powerful live-imaging approaches enable…
Single-molecule stretching experiments on DNA, RNA, and other biological macromolecules opened up the possibility of an impressive progress in many fields of Life and Medical sciences. The reliability of such experiments may be crucially…
A holographic microscope captures interference patterns, or holograms, that encode three-dimensional (3D) information about the object being viewed. Computation is essential to extracting that 3D information. By wrapping low-level…
Molecule-surface interaction is key to many physical and chemical processes at interfaces. Here, we show that the dynamics of single molecules on a surface under ultrahigh vacuum can be resolved using fluorescence imaging. By adapting…
We have developed PyTIE (Python Topological Indices Expressions) which is defined as the collections of Python packages such as PyTIE D, PyTIE DS, PyTIE SMS DE, and PyTIE SMS DSE, which are open-source software packages and cross-platform…
We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…
We have developed a method combining microfluidics, time-lapsed single-molecule microscopy and automated image analysis allowing for the observation of an excess of 3000 complete cell cycles of exponentially growing Escherichia coli cells…
State space models (SSMs) have recently achieved strong performance on long sequence modeling tasks while offering improved memory and computational efficiency compared to transformer based architectures. However, their evaluation has been…
The detection of single molecules has facilitated many advances in life- and material-sciences. Commonly, it founds on the fluorescence detection of single molecules, which are for example attached to the structures under study. For…
I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize…