Image processing tools for petabyte-scale light sheet microscopy data

X Ruan, M Mueller, G Liu, F Görlitz, TM Fu, DE Milkie… - Nature …, 2024 - nature.com
Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of
subcellular dynamics and large biological specimens. However, it often generates datasets …

High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos

P Mukashyaka, P Kumar, DJ Mellert, S Nicholas… - Nature …, 2023 - nature.com
Abstract Three-dimensional (3D) organoid cultures are flexible systems to interrogate
cellular growth, morphology, multicellular spatial architecture, and cellular interactions in …

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

W Saelens, O Pushkarev, B Deplancke - Nature Communications, 2025 - nature.com
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that
fully exploit this property in single-nucleus accessibility data are still lacking. Here, we …

[PDF][PDF] Neurosift: DANDI exploration and NWB visualization in the browser

J Magland, J Soules, C Baker, B Dichter - Journal of Open Source …, 2024 - joss.theoj.org
Neurosift, a browser-based visualization tool, is designed for the interactive exploration of
Neurodata Without Borders (NWB) files, whether stored locally, on remote servers, or within …

Learning precise segmentation of neurofibrillary tangles from rapid manual point annotations

S Ghandian, L Albarghouthi, K Nava, SRR Sharma… - bioRxiv, 2024 - biorxiv.org
Accumulation of abnormal tau protein into neurofibrillary tangles (NFTs) is a pathologic
hallmark of Alzheimer disease. Accurate and efficient detection and quantification of NFTs in …

A harmonized and interoperable format for storing and processing polysomnography data

R Huttunen, M Rusanen, S Nikkonen… - arxiv preprint arxiv …, 2024 - arxiv.org
Polysomnography (PSG) data is recorded and stored in various formats depending on the
recording software. Although the PSG data can usually be exported to open formats, such as …

ITS_LIVE: A Cloud-Native Approach to Monitoring Glaciers From Space

LA López, AS Gardner, CA Greene… - … in Science & …, 2023 - ieeexplore.ieee.org
NASA's ITS_LIVE project delivers information on global glacier dynamics and provides
historical context for climate change with a record of how every glacier in the world has …

Using a Deployable Analysis Environment to Study Continental-Scale Phenology at High-Spatial Resolution

F Nattino, E Izquierdo-Verdiguier… - IGARSS 2024-2024 …, 2024 - ieeexplore.ieee.org
The increasing availability of large open datasets and computational resources offers
unprecedented opportunities for new insight and discoveries. However, researchers are …

SARXarray and STMtools: Open-Source Python Libraries for InSAR Data Processing and Analysis

O Ku, F Alidoost, P Chandramouli… - IGARSS 2024-2024 …, 2024 - ieeexplore.ieee.org
We introduce SARXarray and STMtools, two python libraries designed to support the
exploitation of modern Interferometric Synthetic Aperture Radar (InSAR) data by enabling …