Nature Search

Deep learning enables fast and dense single-molecule localization with high accuracy

DECODE uses deep learning for localizing single emitters in high-density two-dimensional and three-dimensional single-molecule localization microscopy data. DECODE outperforms available methods and enables fast live-cell SMLM of dynamic processes.

Artur Speiser
Lucas-Raphael Müller
Srinivas C. Turaga
Research03 Sept 2021
Nature Methods

Volume: 18, P: 1082-1090
Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy

The cell nucleus coordinates diverse functions. Here, the authors utilise multiplexed super-resolution imaging to study how nuclear proteins are distributed relative to each other from the micro to the nanoscale, providing an approach to understand the organisation of different nuclear environments.

Fariha Rahman
Victoria Augoustides
Wesley R. Legant
ResearchOpen Access01 Jul 2025
Nature Communications

Volume: 16, P: 1-18
Publisher Correction: Deep learning enables fast and dense single-molecule localization with high accuracy

Artur Speiser
Lucas-Raphael Müller
Srinivas C. Turaga
Amendments and Corrections21 Sept 2021
Nature Methods

Volume: 18, P: 1410
Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment

This study combines lattice light sheet microscopy and single molecule imaging to study protein dynamics and chromatin structure in live cells. The authors describe how nucleosomes and proteins move and are organised in relation to chromatin density.

Timothy A. Daugird
Yu Shi
Wesley R. Legant
ResearchOpen Access16 May 2024
Nature Communications

Volume: 15, P: 1-20
3D ATAC-PALM: super-resolution imaging of the accessible genome

3D ATAC-PALM integrates ATAC with super-resolution imaging for nanoscale views of the accessible genome. When combined with FISH, protein fluorescence and genetic perturbation, the method enables investigation of accessible chromatin in situ.

Liangqi Xie
Peng Dong
Zhe Liu
Research16 Mar 2020
Nature Methods

Volume: 17, P: 430-436
Measurement of mechanical tractions exerted by cells in three-dimensional matrices

Tracking the displacement of fluorescent beads surrounding a cell embedded in a hydrogel matrix allows quantitative measurement of the three-dimensional traction forces exerted by the cell.

Wesley R Legant
Jordan S Miller
Christopher S Chen
Research14 Nov 2010
Nature Methods

Volume: 7, P: 969-971
Smart lattice light-sheet microscopy for imaging rare and complex cellular events

smartLLSM uses artificial intelligence-based instrument control to switch between epiflouorescence and lattice light-sheet microscopy to monitor cells at the population level while also capturing multicolor three-dimensional datasets of rare events of interest.

Yu Shi
Jimmy S. Tabet
Wesley R. Legant
Research02 Jan 2024
Nature Methods

Volume: 21, P: 301-310
A quantitative analysis of various patterns applied in lattice light sheet microscopy

Light sheet microscopes reduce phototoxicity and background while improving imaging speed compared to widefield and confocal microscopes. Here the authors quantify the differences between Gaussian and lattice light sheets using simulations and experimental data in fixed and live cells.

Yu Shi
Timothy A. Daugird
Wesley R. Legant
ResearchOpen Access08 Aug 2022
Nature Communications

Volume: 13, P: 1-12
Phase separation drives aberrant chromatin looping and cancer development

The NUP98–HOXA9 oncogenic fusion protein found in leukaemia undergoes phase separation in the nucleus, which helps to promote activation of leukaemic genes and to establish aberrant chromatin looping.

Jeong Hyun Ahn
Eric S. Davis
Gang Greg Wang
Research23 Jun 2021
Nature

Volume: 595, P: 591-595
Degradation-mediated cellular traction directs stem cell fate in covalently crosslinked three-dimensional hydrogels

Adhesive interactions between stem cells and the extracellular matrix are known to regulate stem cell differentiation, yet the underlying mechanisms are not well understood. It is now shown that fate decisions of stem cells encapsulated in covalently crosslinked hydrogels are regulated, independently of matrix mechanics and cell morphology, by the cellular tension generated from cell-induced degradation of the hydrogels.

Sudhir Khetan
Murat Guvendiren
Jason A. Burdick
Research24 Mar 2013
Nature Materials

Volume: 12, P: 458-465
High-density three-dimensional localization microscopy across large volumes

Lattice light-sheet and PAINT microscopy are combined to achieve low-background detection of dense molecular labels, yielding super-resolution localization microscopy images of intricate 3D structures within dividing cells and embryos.

Wesley R Legant
Lin Shao
Eric Betzig
Research07 Mar 2016
Nature Methods

Volume: 13, P: 359-365
Improving probes for super-resolution

Chemically modified DNA aptamers enable quantitative super-resolution imaging.

Regan P. Moore
Wesley R. Legant
News & Views31 Aug 2018
Nature Methods

Volume: 15, P: 659-660
Applying systems-level spectral imaging and analysis to reveal the organelle interactome

Using confocal and lattice light sheet microscopy, the authors perform systems-level analysis of the organelle interactome in live cells, allowing them to visualize the frequency and locality of up to five-way interactions between different organelles.

Alex M. Valm
Sarah Cohen
Jennifer Lippincott-Schwartz
Research24 May 2017
Nature

Volume: 546, P: 162-167
Dynamics of phosphoinositide conversion in clathrin-mediated endocytic traffic

‘Coincidence-detecting’ phosphoinositide sensors are used to study changes in the phosphoinositide lipid species found in membranes during the development and maturation of endocytic clathrin-coated vesicles.

Kangmin He
Robert Marsland III
Tom Kirchhausen
Research13 Dec 2017
Nature

Volume: 552, P: 410-414

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