Universal Inverse Modeling of Point Spread Functions for SMLM Localization and Microscope Characterization

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2024 Jun 3

PMID 38831208

Authors

Sheng Liu

Jianwei Chen

Jonas Hellgoth

Lucas-Raphael Muller

Boris Ferdman

Christian Karras

Dafei Xiao

Keith A Lidke

Rainer Heintzmann

Yoav Shechtman

Yiming Li

Jonas Ries

Affiliations

Soon will be listed here.

Abstract

The point spread function (PSF) of a microscope describes the image of a point emitter. Knowing the accurate PSF model is essential for various imaging tasks, including single-molecule localization, aberration correction and deconvolution. Here we present universal inverse modeling of point spread functions (uiPSF), a toolbox to infer accurate PSF models from microscopy data, using either image stacks of fluorescent beads or directly images of blinking fluorophores, the raw data in single-molecule localization microscopy (SMLM). Our modular framework is applicable to a variety of microscope modalities and the PSF model incorporates system- or sample-specific characteristics, for example, the bead size, field- and depth- dependent aberrations, and transformations among channels. We demonstrate its application in single or multiple channels or large field-of-view SMLM systems, 4Pi-SMLM, and lattice light-sheet microscopes using either bead data or single-molecule blinking data.

Citing Articles

Enabling real-time reconstruction for large field-of-view single-molecule localization microscopy using discrete field-dependent point-spread function.

Lu J, Xu L, Liao S, Wang W, Dong B Biomed Opt Express. 2025; 16(2):718-735.

PMID: 39958841 PMC: 11828444. DOI: 10.1364/BOE.545534.

Calibration-free estimation of field dependent aberrations for single molecule localization microscopy across large fields of view.

Droste I, Schuitema E, Khan S, Heldens S, van Werkhoven B, Lidke K bioRxiv. 2024; .

PMID: 39713420 PMC: 11661230. DOI: 10.1101/2024.12.11.627909.

Single-molecule orientation-localization microscopy: Applications and approaches.

Zhang O, Lew M Q Rev Biophys. 2024; 57:e17.

PMID: 39710866 PMC: 11771422. DOI: 10.1017/S0033583524000167.

Mantis: High-throughput 4D imaging and analysis of the molecular and physical architecture of cells.

Ivanov I, Hirata-Miyasaki E, Chandler T, Cheloor-Kovilakam R, Liu Z, Pradeep S PNAS Nexus. 2024; 3(9):pgae323.

PMID: 39282007 PMC: 11393572. DOI: 10.1093/pnasnexus/pgae323.

Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy.

Dibaji H, Kazemi Nasaban Shotorban A, Grattan R, Lucero S, Schodt D, Lidke K Nat Commun. 2024; 15(1):5019.

PMID: 38866746 PMC: 11169345. DOI: 10.1038/s41467-024-49291-0.

References

Theer P, Mongis C, Knop M . PSFj: know your fluorescence microscope. Nat Methods. 2014; 11(10):981-2. DOI: 10.1038/nmeth.3102. View

Faklaris O, Bancel-Vallee L, Dauphin A, Monterroso B, Frere P, Geny D . Quality assessment in light microscopy for routine use through simple tools and robust metrics. J Cell Biol. 2022; 221(11). PMC: 9526251. DOI: 10.1083/jcb.202107093. View

Qiao S, Bernasek S, Gallagher K, Yamada S, Bagheri N, Amaral L . Energy metabolism modulates the regulatory impact of activators on gene expression. bioRxiv. 2023; . PMC: 10634812. DOI: 10.1101/2023.10.24.563842. View

Guo M, Li Y, Su Y, Lambert T, Dalle Nogare D, Moyle M . Rapid image deconvolution and multiview fusion for optical microscopy. Nat Biotechnol. 2020; 38(11):1337-1346. PMC: 7642198. DOI: 10.1038/s41587-020-0560-x. View

Li Y, Wu Y, Hoess P, Mund M, Ries J . Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization. Biomed Opt Express. 2019; 10(6):2708-2718. PMC: 6583355. DOI: 10.1364/BOE.10.002708. View

Hulleman C, Thorsen R, Kim E, Dekker C, Stallinga S, Rieger B . Simultaneous orientation and 3D localization microscopy with a Vortex point spread function. Nat Commun. 2021; 12(1):5934. PMC: 8505439. DOI: 10.1038/s41467-021-26228-5. View

Zhang O, Guo Z, He Y, Wu T, Vahey M, Lew M . Six-Dimensional Single-Molecule Imaging with Isotropic Resolution using a Multi-View Reflector Microscope. Nat Photonics. 2023; 17(2):179-186. PMC: 10035538. DOI: 10.1038/s41566-022-01116-6. View

Shechtman Y, Weiss L, Backer A, Lee M, Moerner W . Multicolour localization microscopy by point-spread-function engineering. Nat Photonics. 2017; 10:590-594. PMC: 5391844. DOI: 10.1038/nphoton.2016.137. View

Lelek M, Gyparaki M, Beliu G, Schueder F, Griffie J, Manley S . Single-molecule localization microscopy. Nat Rev Methods Primers. 2022; 1. PMC: 9160414. DOI: 10.1038/s43586-021-00038-x. View

10.

Huang B, Wang W, Bates M, Zhuang X . Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science. 2008; 319(5864):810-3. PMC: 2633023. DOI: 10.1126/science.1153529. View

11.

Pavani S, Thompson M, Biteen J, Lord S, Liu N, Twieg R . Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proc Natl Acad Sci U S A. 2009; 106(9):2995-9. PMC: 2651341. DOI: 10.1073/pnas.0900245106. View

12.

Shechtman Y, Sahl S, Backer A, Moerner W . Optimal point spread function design for 3D imaging. Phys Rev Lett. 2014; 113(13):133902. PMC: 4381866. DOI: 10.1103/PhysRevLett.113.133902. View

13.

Juette M, Gould T, Lessard M, Mlodzianoski M, Nagpure B, Bennett B . Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat Methods. 2008; 5(6):527-9. DOI: 10.1038/nmeth.1211. View

14.

Ram S, Prabhat P, Chao J, Ward E, Ober R . High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells. Biophys J. 2008; 95(12):6025-43. PMC: 2599831. DOI: 10.1529/biophysj.108.140392. View

15.

Legant W, Shao L, Grimm J, Brown T, Milkie D, Avants B . High-density three-dimensional localization microscopy across large volumes. Nat Methods. 2016; 13(4):359-65. PMC: 4889433. DOI: 10.1038/nmeth.3797. View

16.

Shtengel G, Galbraith J, Galbraith C, Lippincott-Schwartz J, Gillette J, Manley S . Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc Natl Acad Sci U S A. 2009; 106(9):3125-30. PMC: 2637278. DOI: 10.1073/pnas.0813131106. View

17.

Aquino D, Schonle A, Geisler C, Middendorff C, Wurm C, Okamura Y . Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores. Nat Methods. 2011; 8(4):353-9. DOI: 10.1038/nmeth.1583. View

18.

Smith C, Joseph N, Rieger B, Lidke K . Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat Methods. 2010; 7(5):373-5. PMC: 2862147. DOI: 10.1038/nmeth.1449. View

19.

Mlodzianoski M, Juette M, Beane G, Bewersdorf J . Experimental characterization of 3D localization techniques for particle-tracking and super-resolution microscopy. Opt Express. 2009; 17(10):8264-77. DOI: 10.1364/oe.17.008264. View

20.

Babcock H, Zhuang X . Analyzing Single Molecule Localization Microscopy Data Using Cubic Splines. Sci Rep. 2017; 7(1):552. PMC: 5428856. DOI: 10.1038/s41598-017-00622-w. View