[HTML][HTML] Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

J Dekker, F Alber, S Aufmkolk, BJ Beliveau… - Molecular cell, 2023 - cell.com
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome
and the nucleus in space and time. We summarize progress by the consortium and highlight …

Volume electron microscopy

CJ Peddie, C Genoud, A Kreshuk, K Meechan… - Nature Reviews …, 2022 - nature.com
Life exists in three dimensions, but until the turn of the century most electron microscopy
methods provided only 2D image data. Recently, electron microscopy techniques capable of …

EMPIAR: the electron microscopy public image archive

A Iudin, PK Korir, S Somasundharam… - Nucleic Acids …, 2023 - academic.oup.com
Public archiving in structural biology is well established with the Protein Data Bank (PDB;
wwPDB. org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; …

WashU epigenome browser update 2022

D Li, D Purushotham, JK Harrison, S Hsu… - Nucleic acids …, 2022 - academic.oup.com
Abstract WashU Epigenome Browser (https://epigenomegateway. wustl. edu/browser/) is a
web-based genomic data exploration tool that provides visualization, integration, and …

Volume EM: a quiet revolution takes shape

LM Collinson, C Bosch, A Bullen, JJ Burden… - Nature …, 2023 - nature.com
Volume electron microscopy (vEM) is a group of techniques that reveal the 3D ultrastructure
of cells and tissues through continuous depths of at least 1 micrometer. A burgeoning …

OME-Zarr: a cloud-optimized bioimaging file format with international community support

J Moore, D Basurto-Lozada, S Besson… - Histochemistry and Cell …, 2023 - Springer
A growing community is constructing a next-generation file format (NGFF) for bioimaging to
overcome problems of scalability and heterogeneity. Organized by the Open Microscopy …

The european bioinformatics institute (EMBL-EBI) in 2021

G Cantelli, A Bateman, C Brooksbank… - Nucleic Acids …, 2022 - academic.oup.com
Abstract The European Bioinformatics Institute (EMBL-EBI) maintains a comprehensive
range of freely available and up-to-date molecular data resources, which includes over 40 …

The BioImage archive–building a home for life-sciences microscopy data

M Hartley, GJ Kleywegt, A Patwardhan… - Journal of Molecular …, 2022 - Elsevier
Despite the huge impact of data resources in genomics and structural biology, until now
there has been no central archive for biological data for all imaging modalities. The …

MITI minimum information guidelines for highly multiplexed tissue images

D Schapiro, C Yapp, A Sokolov, SM Reynolds… - Nature …, 2022 - nature.com
The imminent release of tissue atlases combining multichannel microscopy with single-cell
sequencing and other omics data from normal and diseased specimens creates an urgent …

QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

U Boehm, G Nelson, CM Brown, S Bagley, P Bajcsy… - Nature …, 2021 - nature.com
The community-driven initiative Quality Assessment and Reproducibility for Instruments &
Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light …