Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

JW Hickey, EK Neumann, AJ Radtke, JM Camarillo… - Nature …, 2022 - nature.com
Tissues and organs are composed of distinct cell types that must operate in concert to
perform physiological functions. Efforts to create high-dimensional biomarker catalogs of …

Big data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management

D Poger, L Yen, F Braet - Histochemistry and Cell Biology, 2023 - Springer
The second decade of the twenty-first century witnessed a new challenge in the handling of
microscopy data. Big data, data deluge, large data, data compliance, data analytics, data …

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 …

Tracking cell lineages in 3D by incremental deep learning

K Sugawara, Ç Çevrim, M Averof - Elife, 2022 - elifesciences.org
Deep learning is emerging as a powerful approach for bioimage analysis. Its use in cell
tracking is limited by the scarcity of annotated data for the training of deep-learning models …

QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

G Nelson, U Boehm, S Bagley, P Bajcsy… - Journal of …, 2021 - Wiley Online Library
A modern day light microscope has evolved from a tool devoted to making primarily
empirical observations to what is now a sophisticated, quantitative device that is an integral …

Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

M Hammer, M Huisman, A Rigano, U Boehm… - Nature …, 2021 - nature.com
Rigorous record-keeping and quality control are required to ensure the quality,
reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light …

How innovations in methodology offer new prospects for volume electron microscopy

AJ Kievits, R Lane, EC Carroll… - Journal of …, 2022 - Wiley Online Library
Detailed knowledge of biological structure has been key in understanding biology at several
levels of organisation, from organs to cells and proteins. Volume electron microscopy …

Navigating the light-sheet image analysis software landscape: concepts for driving cohesion from data acquisition to analysis

HC Gibbs, SM Mota, NA Hart, SW Min… - Frontiers in Cell and …, 2021 - frontiersin.org
From the combined perspective of biologists, microscope instrumentation developers,
imaging core facility scientists, and high performance computing experts, we discuss the …