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Yeh LH, Ivanov IE, Chandler T, Byrum JR, Chhun BB, Guo SM, Foltz C, Hashemi E, Perez-Bermejo JA, Wang H, Yu Y, Kazansky PG, Conklin BR, Han MH, Mehta SB. Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution. Nat Methods 2024; 21:1257-1274. [PMID: 38890427 PMCID: PMC11239526 DOI: 10.1038/s41592-024-02291-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/24/2024] [Indexed: 06/20/2024]
Abstract
The dry mass and the orientation of biomolecules can be imaged without a label by measuring their permittivity tensor (PT), which describes how biomolecules affect the phase and polarization of light. Three-dimensional (3D) imaging of PT has been challenging. We present a label-free computational microscopy technique, PT imaging (PTI), for the 3D measurement of PT. PTI encodes the invisible PT into images using oblique illumination, polarization-sensitive detection and volumetric sampling. PT is decoded from the data with a vectorial imaging model and a multi-channel inverse algorithm, assuming uniaxial symmetry in each voxel. We demonstrate high-resolution imaging of PT of isotropic beads, anisotropic glass targets, mouse brain tissue, infected cells and histology slides. PTI outperforms previous label-free imaging techniques such as vector tomography, ptychography and light-field imaging in resolving the 3D orientation and symmetry of organelles, cells and tissue. We provide open-source software and modular hardware to enable the adoption of the method.
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Affiliation(s)
- Li-Hao Yeh
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- ASML, San Jose, CA, USA
| | | | | | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- California's Stem Cell Agency, South San Francisco, CA, USA
| | - Bryant B Chhun
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Eikon Therapeutics, Hayward, CA, USA
| | - Syuan-Ming Guo
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Insitro, South San Francisco, CA, USA
| | - Cameron Foltz
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Quantinuum, Broomfield, CO, USA
| | | | - Juan A Perez-Bermejo
- Gladstone Institutes, San Francisco, CA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Yanhao Yu
- University of Southampton, Southampton, UK
| | | | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA
- University of California San Francisco, San Francisco, CA, USA
| | - May H Han
- Stanford University, Palo Alto, CA, USA
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2
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Martínez-Prat B, Arteaga O, Sagués F, Ignés-Mullol J. Multimodal fluorescence microscope with fast adaptive polarimetry. HARDWAREX 2023; 16:e00480. [PMID: 37817881 PMCID: PMC10560837 DOI: 10.1016/j.ohx.2023.e00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 08/02/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
Polarized light microscopy is a widely used technique to observe specimens that are optically anisotropic, or birefringent. It has a broad applicability in the study of minerals, soft materials such as polymers, complex fluids or liquid crystals, and organic tissues in biology and medicine. Most of these observations are qualitative in nature, as it is not obvious to quantify the spatial distribution of optical anisotropy of specimens. Moreover, existing commercial implementations for quantitative polarimetry are costly and slow in nature, precluding real time observation of dynamical processes. Here, we present a custom-made implementation of an optical microscope for quantitative polarimetry at the cost of a standard scientific polarizing microscope. The instrument allows to extract the local optical axis and birefringence of transparent materials with a frequency of several Hz. The instrument is built using off-the-shelf optomechanical components, which optimizes cost, availability, and modularity. An example of the latter is the fact that we combine the polarimetry measurements with simultaneous fluorescence microscopy, which results in a powerful multimodal instrument with broad potential applications.
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Affiliation(s)
- Berta Martínez-Prat
- Universitat de Barcelona and Institute of Nanoscience and Nanotechnology (IN2UB), Martíi Franquès 1, 08028, Barcelona, Spain
| | - Oriol Arteaga
- Universitat de Barcelona and Institute of Nanoscience and Nanotechnology (IN2UB), Martíi Franquès 1, 08028, Barcelona, Spain
| | - Francesc Sagués
- Universitat de Barcelona and Institute of Nanoscience and Nanotechnology (IN2UB), Martíi Franquès 1, 08028, Barcelona, Spain
| | - Jordi Ignés-Mullol
- Universitat de Barcelona and Institute of Nanoscience and Nanotechnology (IN2UB), Martíi Franquès 1, 08028, Barcelona, Spain
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3
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Howard AFD, Huszar IN, Smart A, Cottaar M, Daubney G, Hanayik T, Khrapitchev AA, Mars RB, Mollink J, Scott C, Sibson NR, Sallet J, Jbabdi S, Miller KL. An open resource combining multi-contrast MRI and microscopy in the macaque brain. Nat Commun 2023; 14:4320. [PMID: 37468455 PMCID: PMC10356772 DOI: 10.1038/s41467-023-39916-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
Understanding brain structure and function often requires combining data across different modalities and scales to link microscale cellular structures to macroscale features of whole brain organisation. Here we introduce the BigMac dataset, a resource combining in vivo MRI, extensive postmortem MRI and multi-contrast microscopy for multimodal characterisation of a single whole macaque brain. The data spans modalities (MRI and microscopy), tissue states (in vivo and postmortem), and four orders of spatial magnitude, from microscopy images with micrometre or sub-micrometre resolution, to MRI signals on the order of millimetres. Crucially, the MRI and microscopy images are carefully co-registered together to facilitate quantitative multimodal analyses. Here we detail the acquisition, curation, and first release of the data, that together make BigMac a unique, openly-disseminated resource available to researchers worldwide. Further, we demonstrate example analyses and opportunities afforded by the data, including improvement of connectivity estimates from ultra-high angular resolution diffusion MRI, neuroanatomical insight provided by polarised light imaging and myelin-stained histology, and the joint analysis of MRI and microscopy data for reconstruction of the microscopy-inspired connectome. All data and code are made openly available.
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Affiliation(s)
- Amy F D Howard
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| | - Istvan N Huszar
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Adele Smart
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Michiel Cottaar
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Greg Daubney
- Wellcome Centre for Integrative Neuroimaging, Experimental Psychology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Taylor Hanayik
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Rogier B Mars
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jeroen Mollink
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Connor Scott
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Jerome Sallet
- Wellcome Centre for Integrative Neuroimaging, Experimental Psychology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Saad Jbabdi
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Karla L Miller
- Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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Bernardini A, Trovatelli M, Kłosowski MM, Pederzani M, Zani DD, Brizzola S, Porter A, Rodriguez Y Baena F, Dini D. Reconstruction of ovine axonal cytoarchitecture enables more accurate models of brain biomechanics. Commun Biol 2022; 5:1101. [PMID: 36253409 PMCID: PMC9576772 DOI: 10.1038/s42003-022-04052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/29/2022] [Indexed: 12/03/2022] Open
Abstract
There is an increased need and focus to understand how local brain microstructure affects the transport of drug molecules directly administered to the brain tissue, for example in convection-enhanced delivery procedures. This study reports a systematic attempt to characterize the cytoarchitecture of commissural, long association and projection fibres, namely the corpus callosum, the fornix and the corona radiata, with the specific aim to map different regions of the tissue and provide essential information for the development of accurate models of brain biomechanics. Ovine samples are imaged using scanning electron microscopy combined with focused ion beam milling to generate 3D volume reconstructions of the tissue at subcellular spatial resolution. Focus is placed on the characteristic cytological feature of the white matter: the axons and their alignment in the tissue. For each tract, a 3D reconstruction of relatively large volumes, including a significant number of axons, is performed and outer axonal ellipticity, outer axonal cross-sectional area and their relative perimeter are measured. The study of well-resolved microstructural features provides useful insight into the fibrous organization of the tissue, whose micromechanical behaviour is that of a composite material presenting elliptical tortuous tubular axonal structures embedded in the extra-cellular matrix. Drug flow can be captured through microstructurally-based models using 3D volumes, either reconstructed directly from images or generated in silico using parameters extracted from the database of images, leading to a workflow to enable physically-accurate simulations of drug delivery to the targeted tissue. Imaging and reconstruction of sheep brain axonal cytoarchitecture provides insight for brain biomechanics models that simulate drug delivery and other biological processes governed by interstitial fluid flow and transport.
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Affiliation(s)
- Andrea Bernardini
- Department of Mechanical Engineering, Imperial College London, London, SW7 2AZ, UK.
| | - Marco Trovatelli
- Faculty of Veterinary Medicine, Università degli Studi di Milano Statale, 26900, Lodi, Italy
| | | | - Matteo Pederzani
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133, Milan, Italy
| | - Davide Danilo Zani
- Faculty of Veterinary Medicine, Università degli Studi di Milano Statale, 26900, Lodi, Italy
| | - Stefano Brizzola
- Faculty of Veterinary Medicine, Università degli Studi di Milano Statale, 26900, Lodi, Italy
| | - Alexandra Porter
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
| | | | - Daniele Dini
- Department of Mechanical Engineering, Imperial College London, London, SW7 2AZ, UK.
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Cury J, Smets H, Bouzin C, Doguet P, Vanhoestenberghe A, Delbeke J, Tahry RE, Nonclercq A, Gorza SP. Optical birefringence changes in myelinated and unmyelinated nerves: A comparative study. JOURNAL OF BIOPHOTONICS 2022; 15:e202200028. [PMID: 35703916 DOI: 10.1002/jbio.202200028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
The measurement of birefringence variations related to nerve activity is a promising label-free technique for sensing compound neural action potentials (CNAPs). While widely applied in crustaceans, little is known about its efficiency on mammal peripheral nerves. In this work, birefringence recordings to detect CNAPs, and Stokes parameters measurements were performed in rat and lobster nerves. While single-trial detection of nerve activity in crustaceans was achieved successfully, no optical signal was detected in rats, even after extensive signal filtering and averaging. The Stokes parameters showed that a high degree of polarization of light is maintained in lobster sample, whereas an almost complete light depolarization occurs in rat nerve. Our results indicate that depolarization itself is not sufficient to explain the absence of birefringence signals in rats. We hypothesize that this absence comes from the myelin sheets, which constraint the birefringence changes to only take place at the nodes of Ranvier.
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Affiliation(s)
- Joaquín Cury
- Opera-photonics, Université Libre de Bruxelles, Brussels, Belgium
- Bio-, Electro- and Mechanical Systems (BEAMS), Université Libre de Bruxelles, Brussels, Belgium
| | - Hugo Smets
- Bio-, Electro- and Mechanical Systems (BEAMS), Université Libre de Bruxelles, Brussels, Belgium
| | - Caroline Bouzin
- Université Catholique de Louvain, Institut de Recherche Expérimentale et Clinique (IREC), IREC Imaging Platform (2IP), Brussels, Belgium
| | | | - Anne Vanhoestenberghe
- Aspire Centre for Rehabilitation Engineering and Assistive Technology, University College of London, London, UK
| | - Jean Delbeke
- Department of Neurology, Institute of Neurosciences (IONS), Université Catholique de Louvain, Cliniques Universitaires Saint Luc, Brussels, Belgium
| | - Riëm El Tahry
- Department of Neurology, Institute of Neurosciences (IONS), Université Catholique de Louvain, Cliniques Universitaires Saint Luc, Brussels, Belgium
| | - Antoine Nonclercq
- Bio-, Electro- and Mechanical Systems (BEAMS), Université Libre de Bruxelles, Brussels, Belgium
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Papaioannou S, Medini P. Advantages, Pitfalls, and Developments of All Optical Interrogation Strategies of Microcircuits in vivo. Front Neurosci 2022; 16:859803. [PMID: 35837124 PMCID: PMC9274136 DOI: 10.3389/fnins.2022.859803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022] Open
Abstract
The holy grail for every neurophysiologist is to conclude a causal relationship between an elementary behaviour and the function of a specific brain area or circuit. Our effort to map elementary behaviours to specific brain loci and to further manipulate neural activity while observing the alterations in behaviour is in essence the goal for neuroscientists. Recent advancements in the area of experimental brain imaging in the form of longer wavelength near infrared (NIR) pulsed lasers with the development of highly efficient optogenetic actuators and reporters of neural activity, has endowed us with unprecedented resolution in spatiotemporal precision both in imaging neural activity as well as manipulating it with multiphoton microscopy. This readily available toolbox has introduced a so called all-optical physiology and interrogation of circuits and has opened new horizons when it comes to precisely, fast and non-invasively map and manipulate anatomically, molecularly or functionally identified mesoscopic brain circuits. The purpose of this review is to describe the advantages and possible pitfalls of all-optical approaches in system neuroscience, where by all-optical we mean use of multiphoton microscopy to image the functional response of neuron(s) in the network so to attain flexible choice of the cells to be also optogenetically photostimulated by holography, in absence of electrophysiology. Spatio-temporal constraints will be compared toward the classical reference of electrophysiology methods. When appropriate, in relation to current limitations of current optical approaches, we will make reference to latest works aimed to overcome these limitations, in order to highlight the most recent developments. We will also provide examples of types of experiments uniquely approachable all-optically. Finally, although mechanically non-invasive, all-optical electrophysiology exhibits potential off-target effects which can ambiguate and complicate the interpretation of the results. In summary, this review is an effort to exemplify how an all-optical experiment can be designed, conducted and interpreted from the point of view of the integrative neurophysiologist.
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Ivanov IE, Yeh LH, Perez-Bermejo JA, Byrum JR, Kim JYS, Leonetti MD, Mehta SB. Correlative imaging of the spatio-angular dynamics of biological systems with multimodal instant polarization microscope. BIOMEDICAL OPTICS EXPRESS 2022; 13:3102-3119. [PMID: 35774313 PMCID: PMC9203109 DOI: 10.1364/boe.455770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 05/29/2023]
Abstract
The spatial and angular organization of biological macromolecules is a key determinant, as well as informative readout, of their function. Correlative imaging of the dynamic spatio-angular architecture of cells and organelles is valuable, but remains challenging with current methods. Correlative imaging of spatio-angular dynamics requires fast polarization-, depth-, and wavelength-diverse measurement of intrinsic optical properties and fluorescent labels. We report a multimodal instant polarization microscope (miPolScope) that combines a broadband polarization-resolved detector, automation, and reconstruction algorithms to enable label-free imaging of phase, retardance, and orientation, multiplexed with fluorescence imaging of concentration, anisotropy, and orientation of molecules at diffraction-limited resolution and high speed. miPolScope enabled multimodal imaging of myofibril architecture and contractile activity of beating cardiomyocytes, cell and organelle architecture of live HEK293T and U2OS cells, and density and anisotropy of white and grey matter of mouse brain tissue across the visible spectrum. We anticipate these developments in joint quantitative imaging of density and anisotropy to enable new studies in tissue pathology, mechanobiology, and imaging-based screens.
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Affiliation(s)
- Ivan E. Ivanov
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Li-Hao Yeh
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | | | - Janie R. Byrum
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - James Y. S. Kim
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | | | - Shalin B. Mehta
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
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Shoji M, Wakayama T, Ishida H, Kowa H, Sakaue K, Miura T, Higashiguchi T. Single-shot multispectral birefringence mapping by supercontinuum vector beams. APPLIED OPTICS 2020; 59:7131-7138. [PMID: 32788810 DOI: 10.1364/ao.393419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
We demonstrated a single-shot, multispectral birefringence mapping by use of a supercontinuum (SC) vector beam. The vector beam, which was generated by a pair of axially symmetric wave plates, leads to angular-variant polarization modulation to divide birefringence properties of a sample substrate into Fourier space. This strategy allows multispectral birefringence mapping from a single-shot image captured by a multispectral imaging detector. For SC vector beam analysis, we also compensated the retardance error of the axially symmetric wave plate in the superbroadband spectrum. Resolutions of retardance and azimuthal angle were 0.4° and 0.2°, respectively, and the spatial resolution was 60 µm. Those results are expected to provide us a single-shot, multispectral birefringence mapping with high spatial resolution as compared with using a scanning laser microscope. Our proposal has extendibility to develop high-speed, high-resolution birefringence imaging spectroscopy.
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