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Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Zebrafish are an ideal system to study the effect(s) of chemical, genetic, and environmental perturbations on development due to their high fecundity and fast growth. Recently, single cell sequencing has emerged as a powerful tool to…
The locations of different mRNA molecules can be revealed by multiplexed in situ RNA detection. By assigning detected mRNA molecules to individual cells, it is possible to identify many different cell types in parallel. This in turn enables…
Single-cell RNA sequencing (scRNA-seq) is essential for unraveling cellular heterogeneity and diversity, offering invaluable insights for bioinformatics advancements. Despite its potential, traditional clustering methods in scRNA-seq data…
Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete time points. However, current technologies provide only…
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…
A three-dimensional (3D) scanning velocimetry system is developed to quantify the 3D configurations of particles and their surrounding volumetric, three-component velocity fields. The approach uses a translating laser sheet to rapidly scan…
Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…
Cell clustering is crucial for uncovering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data by identifying cell types and marker genes. Despite its importance, benchmarks for scRNA-seq clustering methods remain…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
A multispectral filter array (MSFA) is one solution for capturing a multispectral image (MSI) in a single shot at low cost. We introduce our optimization method of the spectral sensitivity of the MSFAs and demosaicking, and show a new…
As single-cell RNA sequencing datasets grow in adoption, scale, and complexity, data analysis remains a bottleneck for many research groups. Although frontier AI agents have improved dramatically at software engineering and general data…
Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states…
We describe a straightforward, automated line tracking method to visualize within optical resolution the contour of linear macromolecules as they rearrange shape as a function of time by Brownian diffusion and under external fields such as…
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…
In the fields of nanoscience and nanotechnology, it is important to be able to functionalize surfaces chemically for a wide variety of applications. Scanning tunneling microscopes (STMs) are important instruments in this area used to…
Single-shot X-ray imaging of short-lived nanostructures such as clusters and nanoparticles near a phase transition or non-crystalizing objects such as large proteins and viruses is currently the most elegant method for characterizing their…
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…
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical…
Modern high-throughput single-cell immune profiling technologies, such as flow and mass cytometry and single-cell RNA sequencing can readily measure the expression of a large number of protein or gene features across the millions of cells…