Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Self-supervised deep learning encodes high-resolution features of protein subcellular localization

H Kobayashi, KC Cheveralls, MD Leonetti, LA Royer - Nature methods, 2022 - nature.com
Explaining the diversity and complexity of protein localization is essential to fully understand
cellular architecture. Here we present cytoself, a deep-learning approach for fully self …

Nuclear size and shape control

H Cantwell, G Dey - Seminars in Cell & Developmental Biology, 2022 - Elsevier
The nucleus displays a wide range of sizes and shapes in different species and cell types,
yet its size scaling and many of the key structural constituents that determine its shape are …

Epithelial tissue confinement inhibits cell growth and leads to volume-reducing divisions

J Devany, MJ Falk, LJ Holt, A Murugan, ML Gardel - Developmental cell, 2023 - cell.com
Cell proliferation is a central process in tissue development, homeostasis, and disease, yet
how proliferation is regulated in the tissue context remains poorly understood. Here, we …

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 …

The Allen Cell and Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images

J Chen, L Ding, MP Viana, HW Lee, MF Sluezwski… - BioRxiv, 2018 - biorxiv.org
A continuing challenge in quantitative cell biology is the accurate and robust 3D
segmentation of structures of interest from fluorescence microscopy images in an …

Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

A Rigano, S Ehmsen, SU Öztürk, J Ryan, A Balashov… - Nature …, 2021 - nature.com
For quality, interpretation, reproducibility and sharing value, microscopy images should be
accompanied by detailed descriptions of the conditions that were used to produce them …

Size-scaling promotes senescence-like changes in proteome and organelle content

L Cheng, J Chen, Y Kong, C Tan, R Kafri, M Björklund - BioRxiv, 2021 - biorxiv.org
Senescent cells typically have an enlarged cell size but the reason for this has not been fully
elucidated. As abnormal cell size may alter protein concentrations and cellular functionality …

Data science in cell imaging

MK Driscoll, A Zaritsky - Journal of cell science, 2021 - journals.biologists.com
Cell imaging has entered the 'Big Data'era. New technologies in light microscopy and
molecular biology have led to an explosion in high-content, dynamic and multidimensional …

Improving and evaluating deep learning models of cellular organization

H Sun, X Fu, S Abraham, S Jin, RF Murphy - Bioinformatics, 2022 - academic.oup.com
Motivation Cells contain dozens of major organelles and thousands of other structures,
many of which vary extensively in their number, size, shape and spatial distribution. This …