Evidence map›Paper›PMID 40470476›Full record

ArticleArXiv2025

Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens.

Thayer Alshaabi, Daniel E Milkie, Gaoxiang Liu, Cyna Shirazinejad, Jason L Hong, Kemal Achour, Frederik Görlitz, Ana Milunovic-Jevtic, Cat Simmons, Ibrahim S Abuzahriyeh and 10 more

Abstract readPreprint
PubMed Full text at PMC
In one paragraph

Article in ArXiv, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors.

Thayer AlshaabiHoward Hughes Medical Institute, Ashburn, VA.
Daniel E MilkieHoward Hughes Medical Institute, Ashburn, VA.
Gaoxiang LiuDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Cyna ShirazinejadDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Jason L HongDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Kemal AchourDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Frederik GörlitzDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Ana Milunovic-JevticDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Cat SimmonsDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Ibrahim S AbuzahriyehDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Erin HongDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Samara Erin WilliamsDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Nathanael HarrisonDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Evan HuangDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Eun Seok BaeDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Alison N KillileaDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
David G DrubinDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Ian A SwinburneDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Srigokul UpadhyayulaDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA.
Eric BetzigHoward Hughes Medical Institute, Ashburn, VA.

Funding

Nikon confocal system for improved spatio-dynamic analysis of endocytic trafficking eventsR35GM118149 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI DAVID G DRUBIN · 2016 to 2026
$12.0M
Molecular regulation of fluid pressure homeostasis in the inner earR01DC021710 · NIDCD · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian Andrew Swinburne · 2024 to 2026
$1.6M
NIDCD NIH HHS R01 DC021710NIGMS NIH HHS R35 GM118149
6 · The paper itself

Abstract

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. While wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement, and slow when serially mapping spatially varying aberrations across large fields of view. Here, we introduce AOViFT (Adaptive Optical Vision Fourier Transformer)-a machine learning-based aberration sensing framework built around a 3D multistage Vision Transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time, and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or post-acquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

Identifiers

PMID40470476
PMCPMC12136486

What Socratic holds

Textmetadata
LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.