High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation

Laine, Romain F.; Heil, Hannah S.; Coelho, Simao; Nixon-Abell, Jonathon; Jimenez, Angélique; Wiesner, Theresa; Martínez, Damián; Galgani, Tommaso; Régnier, Louise; Stubb, Aki; Follain, Gautier; Webster, Samantha; Goyette, Jesse; Dauphin, Aurelien; Salles, Audrey; Culley, Siân; Jacquemet, Guillaume; Hajj, Bassam; Leterrier, Christophe; Henriques, Ricardo

doi:10.1038/s41592-023-02057-w

Cited by 24 publications

(11 citation statements)

References 81 publications

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“…7). Understanding the spatial dynamics of labeled chromatin awaits further studies with both improved spatial and time resolution, ideally live cell approaches 61 . Arguably, condensed chromatin is the default chromatin state in higher eukaryotic cells 31 .…”

Section: Discussionmentioning

confidence: 99%

Space-time dynamics of genome replication studied with super-resolved microscopy

Gelléri,

Sterr,

Strickfaden

et al. 2024

Preprint

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Genome replication requires duplication of the complete set of DNA sequences together with nucleosomes and epigenetic signatures. Notwithstanding profound knowledge on mechanistic details of DNA replication, major problems of genome replication have remained unresolved. In this perspective article, we consider the accessibility of replication machines to all DNA sequences in due course, the maintenance of functionally important positional and structural features of chromatid domains during replication, and the rapid transition of CTs into prophase chromosomes with two chromatids. We illustrate this problem with EdU pulse-labeling (10 min) and chase experiments (80 min) performed with mouse myeloblast cells. Following light optical serial sectioning of nuclei with 3D structured illumination microscopy (SIM), seven DNA intensity classes were distinguished as proxies for increasing DNA compaction. In nuclei of cells fixed immediately after the pulse-label, we observed a relative under-representation of EdU-labeled DNA in low DNA density classes, representing the active nuclear compartment (ANC), and an over-representation in high density classes representing the inactive nuclear compartment (INC). Cells fixed after the chase revealed an even more pronounced shift to high DNA intensity classes. This finding contrasts with previous studies of the transcriptional topography demonstrating an under-representation of epigenetic signatures for active chromatin and RNAPII in high DNA intensity classes and their over-representation in low density classes. We discuss these findings in the light of current models viewing CDs either as structural chromatin frameworks or as phase-separated droplets, as well as methodological limitations that currently prevent an integration of this contrasting evidence for the spatial nuclear topography of replication and transcription into a common framework of the dynamic nuclear architecture.

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Section: Discussionmentioning

confidence: 99%

Space-time dynamics of genome replication studied with super-resolved microscopy

Gelléri,

Sterr,

Strickfaden

et al. 2024

Preprint

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“…Inspired by the work of Parthasarathy, whose central insight was that the intensity of any imaged particle is radially symmetric about its center, as well as by the SRRF , and SOFI techniques, we reasoned that using metrics based on the radial symmetry of a detected punctum may enable us to reject false-positive puncta detected due to structured background. Specifically, we reasoned that two metrics relating to radial symmetry could be used to reject false positives.…”

Section: Introductionmentioning

confidence: 99%

RASP: Optimal Single Puncta Detection in Complex Cellular Backgrounds

Fu,

Brock,

Andrews

et al. 2024

J. Phys. Chem. B

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Super-resolution and single-molecule microscopies have been increasingly applied to complex biological systems. A major challenge of these approaches is that fluorescent puncta must be detected in the low signal, high noise, heterogeneous background environments of cells and tissue. We present RASP, Radiality Analysis of Single Puncta, a bioimaging-segmentation method that solves this problem. RASP removes false-positive puncta that other analysis methods detect and detects features over a broad range of spatial scales: from single proteins to complex cell phenotypes. RASP outperforms the state-of-the-art methods in precision and speed using image gradients to separate Gaussianshaped objects from the background. We demonstrate RASP's power by showing that it can extract spatial correlations between microglia, neurons, and α-synuclein oligomers in the human brain. This sensitive, computationally efficient approach enables fluorescent puncta and cellular features to be distinguished in cellular and tissue environments, with sensitivity down to the level of the single protein. Python and MATLAB codes, enabling users to perform this RASP analysis on their own data, are provided as Supporting Information and links to third-party repositories.

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“…algorithms [4,9,13], or deploying additional data priors with deep learning techniques [3,7,18,23,26,30,31]. However, because these methods collect less data, they come with additional trade-offs such as reduced resolution or cross-talk.…”

Section: Introductionmentioning

confidence: 99%

Neural space-time model for dynamic scene recovery in multi-shot computational imaging systems

Cao,

Divekar,

Nuñez

et al. 2024

Preprint

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Computational imaging reconstructions from multiple measurements that are captured sequentially often suffer from motion artifacts if the scene is dynamic. We propose a neural space-time model (NSTM) that jointly estimates the scene and its motion dynamics. Hence, we can both remove motion artifacts and resolve sample dynamics. We demonstrate NSTM in three computational imaging systems: differential phase contrast microscopy, 3D structured illumination microscopy, and rolling-shutter DiffuserCam. We show that NSTM can recover subcellular motion dynamics and thus reduce the misinterpretation of living systems caused by motion artifacts.

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High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation

Cited by 24 publications

References 81 publications

Space-time dynamics of genome replication studied with super-resolved microscopy

Space-time dynamics of genome replication studied with super-resolved microscopy

RASP: Optimal Single Puncta Detection in Complex Cellular Backgrounds

Neural space-time model for dynamic scene recovery in multi-shot computational imaging systems

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