Related papers: smFISH_batchRun: A smFISH image processing tool fo…
In this paper we describe the main features of the software package named FITSH, intended to provide a standalone environment for analysis of data acquired by imaging astronomical detectors. The package provides utilities both for the full…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…
Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…
Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains…
To assist researchers to identify Environmental Microorganisms (EMs) effectively, a Multiscale CNN-CRF (MSCC) framework for the EM image segmentation is proposed in this paper. There are two parts in this framework: The first is a novel…
Scanning tunnelling microscopy (STM) is a powerful technique for imaging surfaces with atomic resolution, providing insight into physical and chemical processes at the level of single atoms and molecules. A regular task of STM image…
We here propose an automated pipeline for the microscopy image-based characterization of catalytically active inclusion bodies (CatIBs), which includes a fully automatic experimental high-throughput workflow combined with a hybrid approach…
Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional…
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of…
We outline a simple procedure designed for \emph{automatically} finding sets of multiple images in strong lensing (SL) clusters. We show that by combining (a) an arc-finding (or source extracting) program, (b) photometric redshift…
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various…
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…
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…
Recent technological advances in cutting-edge ultrasensitive fluorescence microscopy have allowed single-molecule imaging experiments in living cells across all three domains of life to become commonplace. Single-molecule live-cell data is…
Multiplexed immunofluorescence microscopy captures detailed measurements of spatially resolved, multiple biomarkers simultaneously, revealing tissue composition and cellular interactions in situ among single cells. The growing scale and…
We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation and pulsed fields. Using Langevin Dynamics simulations, we show that it is possible to design pulsed…
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become…
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing…
Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…
Multiplex brightfield imaging offers the advantage of simultaneously analyzing multiple biomarkers on a single slide, as opposed to single biomarker labeling on multiple consecutive slides. To accurately analyze multiple biomarkers…