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Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Elasmobranchs (shark sand rays) represent a critical component of marine ecosystems. Yet, they are experiencing global population declines and effective monitoring of populations is essential to their protection. Underwater stationary…
Generally, microscopy image analysis in biology relies on the segmentation of individual nuclei, using a dedicated stained image, to identify individual cells. However stained nuclei have drawbacks like the need for sample preparation, and…
Visual analysis of complex fish habitats is an important step towards sustainable fisheries for human consumption and environmental protection. Deep Learning methods have shown great promise for scene analysis when trained on large-scale…
This work proposes SAMSelect, an algorithm to obtain a salient three-channel visualization for multispectral images. We develop SAMSelect and show its use for marine scientists visually interpreting floating marine debris in Sentinel-2…
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
Recent advances in scanning transmission electron and scanning tunneling microscopies allow researchers to measure materials structural and electronic properties, such as atomic displacements and charge density modulations, at an Angstrom…
Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning…
Nanoparticle superlattices consisting of ordered arrangements of nanoparticles exhibit unique optical, magnetic, and electronic properties arising from nanoparticle characteristics as well as their collective behaviors. Understanding how…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
Background: Single-particle cryo-electron microscopy (cryo-EM) has become a popular tool for structural determination of biological macromolecular complexes. High-resolution cryo-EM reconstruction often requires hundreds of thousands of…
We introduce Sashimi plots, a quantitative multi-sample visualization of mRNA sequencing reads aligned to gene annotations. Sashimi plots are made using alignments (stored in the SAM/BAM format) and gene model annotations (in GFF format),…
The spread of microbial infections is governed by the self-organization of bacteria on surfaces. Limitations of live imaging techniques make collective behaviors in clinically relevant systems challenging to quantify. Here, novel…
Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly…
Schemes for X-ray imaging single protein molecules using new x-ray sources, like x-ray free electron lasers (XFELs), require processing many frames of data that are obtained by taking temporally short snapshots of identical molecules, each…
This paper presents DeepFLASH, a novel network with efficient training and inference for learning-based medical image registration. In contrast to existing approaches that learn spatial transformations from training data in the high…
Characterisation of rare microstructural features in scanning electron microscopy (SEM) requires imaging large areas at high resolution. This leads to prohibitively long acquisition times. We present an open-source Python framework that…
Deconvolution of cell mixtures in "bulk" transcriptomic samples from homogenate human tissue is important for understanding the pathologies of diseases. However, several experimental and computational challenges remain in developing and…
Sketch-based streaming algorithms allow efficient processing of big data. These algorithms use small fixed-size storage to store a summary ("sketch") of the input data, and use probabilistic algorithms to estimate the desired quantity.…
Accurate segmentation of 3-D cell nuclei in microscopy images is essential for the study of nuclear organization, gene expression, and cell morphodynamics. Current image segmentation methods are challenged by the complexity and variability…