Evidence map›Paper›PMID 40835649›Full record

ArticleScientific reports2025

DHPSFU: a Fiji plugin for fast and accurate double helix-PSF 3D single-molecule localisation microscopy.

Ziwei Zhang, Aleksandra Ochirova, Siqi Liu, Alex D Herbert, Yunzhao Wu, Wayne Boucher, Steven F Lee, Ernest D Laue, David Klenerman, Aleks Ponjavic

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Ziwei Zhang *Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Aleksandra Ochirova *Department of Biochemistry, University of Cambridge, Cambridge, UK.
Siqi LiuSchool of Physics and Astronomy, University of St. Andrews, St Andrews, UK.
Alex D HerbertChromosome Dynamics and Stability Group, Genome Damage and Stability Centre, University of Sussex, Brighton, UK.
Yunzhao WuYusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Wayne BoucherDepartment of Biochemistry, University of Cambridge, Cambridge, UK.
Steven F LeeYusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Ernest D LaueDepartment of Biochemistry, University of Cambridge, Cambridge, UK.
David KlenermanYusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
Aleks PonjavicSchool of Physics and Astronomy, University of Leeds, Leeds, UK. a.ponjavic@leeds.ac.uk.

Funding

Academy of Medical Sciences SBF0061138Cancer Research UK EDDAPA-2024/100006Engineering and Physical Sciences Research Council EP/W015005/1Medical Research Council MR/P019471/1Wellcome TrustWellcome Trust 206291/Z/17/Z
6 · The paper itself

Abstract

The double-helix point-spread function (DH-PSF) is one of the most used PSFs for large depth-of-field 3D single-molecule localisation microscopy. Due to its popularity, many algorithms have been developed to analyse experimental DH-PSF data, either based on dedicated DH-PSF fitting or on generalised PSF fitting, typically using cubic splines. We show here that the most popular implementations of both these approaches have limitations in terms of localisation performance, processing speed or user-friendliness. To overcome some of these limitations, we have developed a new analytical approach for DH-PSF fitting based on unmixing (DHPSFU) of fitted localisation data using distance pairing. We compare DHPSFU with two popular algorithms, SMAP and EasyDHPSF, using realistic simulated datasets based on experimental data, to show that our algorithm achieves the highest Jaccard index (DHPSFU: 0.98; SMAP: 0.91; EasyDHPSF: 0.85) and fastest CPU-based processing speed (DHPSFU: 6,800 locs/s; SMAP: 2,500 locs/s; EasyDHPSF: 63 locs/s). We also show that our algorithm achieves the best resolution when imaging the cellular plasma membrane of Jurkat T cells (DHPSFU: 140 nm, EasyDHPSF: 162 nm, SMAP: 165 nm). We have incorporated DHPSFU as a Fiji plugin and provide Matlab and Python scripts for user customisation.

Indexed as

Image Processing, Computer-AssistedImaging, Three-DimensionalSingle Molecule ImagingSoftwareAlgorithmsHumansMicroscopy, Fluorescence

Identifiers

PMID40835649
PMCPMC12368115

What Socratic holds

Textmetadata
LicenceCC BY
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Registered trials

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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.