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Gao HC, Xu F, Cheng X, Bi C, Zheng Y, Li Y, Chen T, Li Y, Chubykin AA, Huang F. Interferometric Ultra-High Resolution 3D Imaging through Brain Sections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.03.636258. [PMID: 39975253 PMCID: PMC11838448 DOI: 10.1101/2025.02.03.636258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Single-molecule super-resolution microscopy allows pin-pointing individual molecular positions in cells with nanometer precision. However, achieving molecular resolution through tissues is often difficult because of optical scattering and aberrations. We introduced 4Pi single-molecule nanoscopy for brain with in-situ point spread function retrieval through opaque tissue (4Pi-BRAINSPOT), integrating 4Pi single-molecule switching nanoscopy with dynamic in-situ coherent PSF modeling, single-molecule compatible tissue clearing, light-sheet illumination, and a novel quantitative analysis pipeline utilizing the highly accurate 3D molecular coordinates. This approach enables the quantification of protein distribution with sub-15-nm resolution in all three dimensions in complex tissue specimens. We demonstrated 4Pi-BRAINSPOT's capacities in revealing the molecular arrangements in various sub-cellular organelles and resolved the membrane morphology of individual dendritic spines through 50-μm transgenic mouse brain slices. This ultra-high-resolution approach allows us to decipher nanoscale organelle architecture and molecular distribution in both isolated cells and native tissue environments with precision down to a few nanometers.
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Affiliation(s)
- Hao-Cheng Gao
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Fan Xu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xi Cheng
- Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Cheng Bi
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Yue Zheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Yilun Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Tailong Chen
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yumian Li
- School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
| | | | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
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Cheng X, Nareddula S, Gao HC, Chen Y, Xiao T, Nadew YY, Xu F, Edens PA, Quinn CJ, Kimbrough A, Huang F, Chubykin AA. Impaired Experience-Dependent Theta Oscillation Synchronization and Inter-Areal Synaptic Connectivity in the Visual Cortex of Fmr1 KO Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.601989. [PMID: 39211264 PMCID: PMC11360911 DOI: 10.1101/2024.07.23.601989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Fragile X syndrome (FX) is the most prevalent inheritable form of autism spectrum disorder (ASD), characterized by hypersensitivity, difficulty in habituating to new sensory stimuli, and intellectual disability. Individuals with FX often experience visual perception and learning deficits. Visual experience leads to the emergence of the familiarity-evoked theta band oscillations in the primary visual cortex (V1) and the lateromedial area (LM) of mice. These theta oscillations in V1 and LM are synchronized with each other, providing a mechanism of sensory multi-areal binding. However, how this multi-areal binding and the corresponding theta oscillations are altered in FX is not known. Using iDISCO whole brain clearing with light-sheet microscopy, we quantified immediate early gene Fos expression in V1 and LM, identifying deficits in experience-dependent neural activity in FX mice. We performed simultaneous in vivo recordings with silicon probes in V1 and LM of awake mice and channelrhodopsin-2-assisted circuit mapping (CRACM) in acute brain slices to examine the neural activity and strength of long-range synaptic connections between V1 and LM in both wildtype (WT) and Fmr1 knockout (KO) mice, the model of FX, before and after visual experience. Our findings reveal synchronized familiarity-evoked theta oscillations in V1 and LM, the increased strength of V1→LM functional and synaptic connections, which correlated with the corresponding changes of presynaptic short-term plasticity in WT mice. The LM oscillations were attenuated in FX mice and correlated with impaired functional and synaptic connectivity and short-term plasticity in the feedforward (FF) V1→LM and feedback (FB) LM→V1 pathways. Finally, using 4Pi single-molecule localization microscopy (SMLM) in thick brain tissue, we identified experience-dependent changes in the density and shape of dendritic spines in layer 5 pyramidal cells of WT mice, which correlated with the functional synaptic measurements. Interestingly, there was an increased dendritic spine density and length in naïve FX mice that failed to respond to experience. Our study provides the first comprehensive characterization of the role of visual experience in triggering inter-areal neural synchrony and shaping synaptic connectivity in WT and FX mice.
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Zhang P, Ma D, Cheng X, Tsai AP, Tang Y, Gao HC, Fang L, Bi C, Landreth GE, Chubykin AA, Huang F. Deep learning-driven adaptive optics for single-molecule localization microscopy. Nat Methods 2023; 20:1748-1758. [PMID: 37770712 PMCID: PMC10630144 DOI: 10.1038/s41592-023-02029-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/23/2023] [Indexed: 09/30/2023]
Abstract
The inhomogeneous refractive indices of biological tissues blur and distort single-molecule emission patterns generating image artifacts and decreasing the achievable resolution of single-molecule localization microscopy (SMLM). Conventional sensorless adaptive optics methods rely on iterative mirror changes and image-quality metrics. However, these metrics result in inconsistent metric responses and thus fundamentally limit their efficacy for aberration correction in tissues. To bypass iterative trial-then-evaluate processes, we developed deep learning-driven adaptive optics for SMLM to allow direct inference of wavefront distortion and near real-time compensation. Our trained deep neural network monitors the individual emission patterns from single-molecule experiments, infers their shared wavefront distortion, feeds the estimates through a dynamic filter and drives a deformable mirror to compensate sample-induced aberrations. We demonstrated that our method simultaneously estimates and compensates 28 wavefront deformation shapes and improves the resolution and fidelity of three-dimensional SMLM through >130-µm-thick brain tissue specimens.
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Affiliation(s)
- Peiyi Zhang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Donghan Ma
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Xi Cheng
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Andy P Tsai
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yu Tang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Hao-Cheng Gao
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Li Fang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Cheng Bi
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Gary E Landreth
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Alexander A Chubykin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA.
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA.
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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Zhang Q, Hu Q, Berlage C, Kner P, Judkewitz B, Booth M, Ji N. Adaptive optics for optical microscopy [Invited]. BIOMEDICAL OPTICS EXPRESS 2023; 14:1732-1756. [PMID: 37078027 PMCID: PMC10110298 DOI: 10.1364/boe.479886] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 05/03/2023]
Abstract
Optical microscopy is widely used to visualize fine structures. When applied to bioimaging, its performance is often degraded by sample-induced aberrations. In recent years, adaptive optics (AO), originally developed to correct for atmosphere-associated aberrations, has been applied to a wide range of microscopy modalities, enabling high- or super-resolution imaging of biological structure and function in complex tissues. Here, we review classic and recently developed AO techniques and their applications in optical microscopy.
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Affiliation(s)
- Qinrong Zhang
- Department of Physics, Department of Molecular & Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Qi Hu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Caroline Berlage
- Charité - Universitätsmedizin Berlin, Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, 10099 Berlin, Germany
| | - Peter Kner
- School of Electrical and Computer Engineering, University of Georgia, Athens, GA 30602, USA
| | - Benjamin Judkewitz
- Charité - Universitätsmedizin Berlin, Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, 10117 Berlin, Germany
| | - Martin Booth
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Na Ji
- Department of Physics, Department of Molecular & Cellular Biology, University of California, Berkeley, CA 94720, USA
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Bates M, Keller-Findeisen J, Przybylski A, Hüper A, Stephan T, Ilgen P, Cereceda Delgado AR, D'Este E, Egner A, Jakobs S, Sahl SJ, Hell SW. Optimal precision and accuracy in 4Pi-STORM using dynamic spline PSF models. Nat Methods 2022; 19:603-612. [PMID: 35577958 PMCID: PMC9119851 DOI: 10.1038/s41592-022-01465-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022]
Abstract
Coherent fluorescence imaging with two objective lenses (4Pi detection) enables single-molecule localization microscopy with sub-10 nm spatial resolution in three dimensions. Despite its outstanding sensitivity, wider application of this technique has been hindered by complex instrumentation and the challenging nature of the data analysis. Here we report the development of a 4Pi-STORM microscope, which obtains optimal resolution and accuracy by modeling the 4Pi point spread function (PSF) dynamically while also using a simpler optical design. Dynamic spline PSF models incorporate fluctuations in the modulation phase of the experimentally determined PSF, capturing the temporal evolution of the optical system. Our method reaches the theoretical limits for precision and minimizes phase-wrapping artifacts by making full use of the information content of the data. 4Pi-STORM achieves a near-isotropic three-dimensional localization precision of 2–3 nm, and we demonstrate its capabilities by investigating protein and nucleic acid organization in primary neurons and mammalian mitochondria. A dynamic model of the 4Pi point spread function enables localization microscopy with exceptional three-dimensional resolution and a simpler optical design. 4Pi-STORM images of neurons and mitochondria reveal new details of nanoscale protein and nucleic acid organization.
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Affiliation(s)
- Mark Bates
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. .,Department of Optical Nanoscopy, Institute for NanoPhotonics, Göttingen, Germany.
| | - Jan Keller-Findeisen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Adrian Przybylski
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Andreas Hüper
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Clinic of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Peter Ilgen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Clinic of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Angel R Cereceda Delgado
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Alexander Egner
- Department of Optical Nanoscopy, Institute for NanoPhotonics, Göttingen, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Clinic of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Steffen J Sahl
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. .,Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany.
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Cremer C, Birk U. Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A: MATHEMATICAL, PHYSICAL AND ENGINEERING SCIENCES 2022; 380:20210152. [PMID: 0 DOI: 10.1098/rsta.2021.0152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/02/2021] [Indexed: 05/19/2023]
Abstract
Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Christoph Cremer
- Max-Planck Institute for Polymer Research, and Institute of Molecular Biology (IMB), D-55128 Mainz, Germany
- Kirchhoff Institute for Physics (KIP), Interdisciplinary Center for Scientific Computing (IWR), and Institute of Pharmacy and Molecular Biotechnology (IPMB), University Heidelberg, D-69120 Heidelberg, Germany
| | - Udo Birk
- Institute for Photonics and ICT (IPI), University of Applied Sciences (FH Graubünden), CH-7000 Chur, Switzerland
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Abstract
Super-resolution microscopy techniques, and specifically single-molecule localization microscopy (SMLM), are approaching nanometer resolution inside cells and thus have great potential to complement structural biology techniques such as electron microscopy for structural cell biology. In this review, we introduce the different flavors of super-resolution microscopy, with a special emphasis on SMLM and MINFLUX (minimal photon flux). We summarize recent technical developments that pushed these localization-based techniques to structural scales and review the experimental conditions that are key to obtaining data of the highest quality. Furthermore, we give an overview of different analysis methods and highlight studies that used SMLM to gain structural insights into biologically relevant molecular machines. Ultimately, we give our perspective on what is needed to push the resolution of these techniques even further and to apply them to investigating dynamic structural rearrangements in living cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sheng Liu
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
| | - Philipp Hoess
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
| | - Jonas Ries
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
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8
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Implementation of a 4Pi-SMS super-resolution microscope. Nat Protoc 2020; 16:677-727. [PMID: 33328610 DOI: 10.1038/s41596-020-00428-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022]
Abstract
The development of single-molecule switching (SMS) fluorescence microscopy (also called single-molecule localization microscopy) over the last decade has enabled researchers to image cell biological structures at unprecedented resolution. Using two opposing objectives in a so-called 4Pi geometry doubles the available numerical aperture, and coupling this with interferometric detection has demonstrated 3D resolution down to 10 nm over entire cellular volumes. The aim of this protocol is to enable interested researchers to establish 4Pi-SMS super-resolution microscopy in their laboratories. We describe in detail how to assemble the optomechanical components of a 4Pi-SMS instrument, align its optical beampath and test its performance. The protocol further provides instructions on how to prepare test samples of fluorescent beads, operate this instrument to acquire images of whole cells and analyze the raw image data to reconstruct super-resolution 3D data sets. Furthermore, we provide a troubleshooting guide and present examples of anticipated results. An experienced optical instrument builder will require ~12 months from the start of ordering hardware components to acquiring high-quality biological images.
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Möckl L, Moerner WE. Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges. J Am Chem Soc 2020; 142:17828-17844. [PMID: 33034452 PMCID: PMC7582613 DOI: 10.1021/jacs.0c08178] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 12/31/2022]
Abstract
Single-molecule super-resolution microscopy has developed from a specialized technique into one of the most versatile and powerful imaging methods of the nanoscale over the past two decades. In this perspective, we provide a brief overview of the historical development of the field, the fundamental concepts, the methodology required to obtain maximum quantitative information, and the current state of the art. Then, we will discuss emerging perspectives and areas where innovation and further improvement are needed. Despite the tremendous progress, the full potential of single-molecule super-resolution microscopy is yet to be realized, which will be enabled by the research ahead of us.
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Affiliation(s)
- Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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Li Y, Buglakova E, Zhang Y, Thevathasan JV, Bewersdorf J, Ries J. Accurate 4Pi single-molecule localization using an experimental PSF model. OPTICS LETTERS 2020; 45:3765-3768. [PMID: 32630949 DOI: 10.1364/ol.397754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Interferometric single-molecule localization microscopy (iPALM, 4Pi-SMS) uses multiphase interferometry to localize single fluorophores and achieves nanometer isotropic resolution in 3D. The current data analysis workflow, however, fails to reach the theoretical resolution limit due to the suboptimal localization algorithm. Here, we develop a method to fit an experimentally derived point spread function (PSF) model to the interference 4Pi-PSF. As the interference phase is not fixed with respect to the shape of the PSF, we decoupled the phase term in the model from the 3D position of the PSF. The fitter can reliably infer the interference period even without introducing astigmatism, reducing the complexity of the microscope. Using a spline-interpolated experimental PSF model and by fitting all phase images globally, we show on simulated data that we can achieve the theoretical limit of 3D resolution, the Cramér-Rao lower bound (CRLB), also for the 4Pi microscope.
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