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Article ; Online: Microscopy. The superresolved brain.

Dodt, Hans-Ulrich

2015 Volume 347, Issue 6221, Page(s) 474–475

MeSH term(s)	Animals ; Coated Pits, Cell-Membrane/ultrastructure ; Hippocampus/ultrastructure ; Humans ; Microscopy/methods ; Microtubules/ultrastructure ; Optical Imaging/methods
Language	English
Publishing date	2015-01-29
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aaa5084
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: FlyClear: A Tissue-Clearing Technique for High-Resolution Microscopy of Drosophila.

Pende, Marko / Saghafi, Saiedeh / Becker, Klaus / Hummel, Thomas / Dodt, Hans-Ulrich

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2540, Page(s) 349–359

Abstract: Fluorescently labeled transgenic lines of Drosophila melanogaster are a powerful routine tool in fly laboratories. The possibility to fluorescently visualize individual cell populations or entire tissues and the constantly improving microscopy ... ...

Abstract	Fluorescently labeled transgenic lines of Drosophila melanogaster are a powerful routine tool in fly laboratories. The possibility to fluorescently visualize individual cell populations or entire tissues and the constantly improving microscopy technologies such as two-photon or light-sheet applications, with deep tissue imaging, hold great potential to address central biological questions at an organismic level. However, strong pigmentation and the opaque nature of the D. melanogaster cuticle hinder the penetration of visible light into internal tissues, thereby limiting the application of fluorescent microscopes to analyses of the outermost surfaces of intact samples. In addition, tissue-induced light scattering and optical aberrations quickly blur the view and, hence, require tissue sectioning for further investigation. We have developed a tissue-clearing and depigmentation approach (FlyClear), which preserves endogenous fluorescent signals and is applicable to various developmental stages ranging from larvae to adult fruit flies (Pende et al. Nature communications 9:4731, 2018). In this chapter, we provide a detailed protocol of the experimental steps involved.
MeSH term(s)	Animals ; Animals, Genetically Modified ; Drosophila ; Drosophila melanogaster ; Imaging, Three-Dimensional/methods ; Larva ; Microscopy, Fluorescence/methods
Language	English
Publishing date	2022-08-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2541-5_18
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The superresolved brain

Dodt, Hans-Ulrich

Science. 2015 Jan. 30, v. 347, no. 6221

2015

Abstract: In the past decade, important advances have been made to increase the resolution of the light microscope, as acknowledged by last year's Nobel Prize for superresolved fluorescence microscopy (1 , 2). This progress is fascinating but comes at the price of ...

Abstract	In the past decade, important advances have been made to increase the resolution of the light microscope, as acknowledged by last year's Nobel Prize for superresolved fluorescence microscopy (1 , 2). This progress is fascinating but comes at the price of high illumination intensities or long recording times, and expensive instruments. As reported on page 543 of this issue, Chen et al. (3) have cleverly turned the problem around by asking: What if we leave the microscope as it is, and increase the object instead?
Keywords	brain ; fluorescence microscopy ; light intensity ; Nobel Prize ; prices
Language	English
Dates of publication	2015-0130
Size	p. 474-475.
Publishing place	American Association for the Advancement of Science
Document type	Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aaa5084
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Engineering a better light sheet in an axicon-based system using a flattened Gaussian beam of low order.

Saghafi, Saiedeh / Becker, Klaus / Gori, Franco / Foroughipour, Massih / Bollwein, Christine / Foroughipour, Meraaj / Steiger, Katja / Weichert, Wilko / Dodt, Hans-Ulrich

Journal of biophotonics

2022 Volume 15, Issue 6, Page(s) e202100342

Abstract: Lasers are fundamental tools in research and development. The shape of an incident laser beam directly affects the results, when it propagates through complex structured meso-aspheric optical elements. In conic-based systems utilizing elements such as ... ...

Abstract	Lasers are fundamental tools in research and development. The shape of an incident laser beam directly affects the results, when it propagates through complex structured meso-aspheric optical elements. In conic-based systems utilizing elements such as axicons, the impact of secondary lobes is mostly overlooked, although the intensity distributions at the central spot and the side-lobes directly affect the beam properties. We investigate the interaction of two axicons (160° and 170°) with incident beams approximated by Gaussian, high-order Flattened-Gaussian, and low-order Flattened-Gaussian functions. We demonstrate that replacing an incident Gaussian beam with a low-order Flattened-Gaussian beam reduces the secondary lobes and significantly improves the uniformity of the intensity profile. We practically applied this effect in engineering a conic-aspheric-based static light-sheet microscope producing markedly improved results.
MeSH term(s)	Lasers ; Microscopy ; Normal Distribution ; Optical Devices
Language	English
Publishing date	2022-02-25
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2390063-5
ISSN	1864-0648 ; 1864-063X
ISSN (online)	1864-0648
ISSN	1864-063X
DOI	10.1002/jbio.202100342
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Article ; Online: Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy.

Ueda, Hiroki R / Dodt, Hans-Ulrich / Osten, Pavel / Economo, Michael N / Chandrashekar, Jayaram / Keller, Philipp J

Neuron

2020 Volume 106, Issue 3, Page(s) 369–387

Abstract: Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized ...

Abstract	Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.
MeSH term(s)	Animals ; Brain/cytology ; Brain/physiology ; Humans ; Imaging, Three-Dimensional/methods ; Microscopy/methods ; Optical Imaging/methods ; Staining and Labeling/methods
Language	English
Publishing date	2020-05-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	808167-0
ISSN	1097-4199 ; 0896-6273
ISSN (online)	1097-4199
ISSN	0896-6273
DOI	10.1016/j.neuron.2020.03.004
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Article ; Online: Light-Sheet Fluorescence Microscopy: Chemical Clearing and Labeling Protocols for Ultramicroscopy.

Jährling, Nina / Becker, Klaus / Saghafi, Saiedeh / Dodt, Hans-Ulrich

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1563, Page(s) 33–49

Abstract: Light-sheet microscopy is an effective technique in neuroscience, developmental biology, and cancer research for visualizing and analyzing cellular networks and whole organs in three dimensions. Because this technique requires specimens to be translucent ...

Abstract	Light-sheet microscopy is an effective technique in neuroscience, developmental biology, and cancer research for visualizing and analyzing cellular networks and whole organs in three dimensions. Because this technique requires specimens to be translucent they commonly have to be cleared before microscopy inspection. Here, we provide 3DISCO based protocols for preparing cleared samples of immuno-stained neural networks, lectin-labeled vascular networks, and Methoxy-X04 labeled beta-amyloid plaques in mice. 3DISCO utilizes the lipophilic solvents tetrahydrofuran (THF) and dibenzylether (DBE) for dehydration and successive clearing. Crucial steps for obtaining transparent tissues and preserving the fragile endogenous GFP are the transcardial perfusion, as well as the proper implementation of the 3DISCO clearing process using peroxide free chemicals. We further provide a protocol for resin embedding of 3DISCO cleared specimens that allows long term archiving of samples for years with virtually no loss in signal quality.
MeSH term(s)	Animals ; Brain ; Imaging, Three-Dimensional ; Immunohistochemistry/methods ; Mice ; Microscopy, Fluorescence/instrumentation ; Microscopy, Fluorescence/methods ; Spinal Cord
Language	English
Publishing date	2017-03-18
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-6810-7_3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Light sheet microscopy of living or cleared specimens.

Keller, Philipp J / Dodt, Hans-Ulrich

Current opinion in neurobiology

2012 Volume 22, Issue 1, Page(s) 138–143

Abstract: Light sheet microscopy is a versatile imaging technique with a unique combination of capabilities. It provides high imaging speed, high signal-to-noise ratio and low levels of photobleaching and phototoxic effects. These properties are crucial in a wide ... ...

Abstract	Light sheet microscopy is a versatile imaging technique with a unique combination of capabilities. It provides high imaging speed, high signal-to-noise ratio and low levels of photobleaching and phototoxic effects. These properties are crucial in a wide range of applications in the life sciences, from live imaging of fast dynamic processes in single cells to long-term observation of developmental dynamics in entire large organisms. When combined with tissue clearing methods, light sheet microscopy furthermore allows rapid imaging of large specimens with excellent coverage and high spatial resolution. Even samples up to the size of entire mammalian brains can be efficiently recorded and quantitatively analyzed. Here, we provide an overview of the history of light sheet microscopy, review the development of tissue clearing methods, and discuss recent technical breakthroughs that have the potential to influence the future direction of the field.
MeSH term(s)	History, 20th Century ; Microscopy/history ; Microscopy/instrumentation ; Microscopy/methods
Language	English
Publishing date	2012-02
Publishing country	England
Document type	Historical Article ; Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1078046-4
ISSN	1873-6882 ; 0959-4388
ISSN (online)	1873-6882
ISSN	0959-4388
DOI	10.1016/j.conb.2011.08.003
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Zs.A 3260: Show issues

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Article ; Online: A hypothalamic dopamine locus for psychostimulant-induced hyperlocomotion in mice.

Korchynska, Solomiia / Rebernik, Patrick / Pende, Marko / Boi, Laura / Alpár, Alán / Tasan, Ramon / Becker, Klaus / Balueva, Kira / Saghafi, Saiedeh / Wulff, Peer / Horvath, Tamas L / Fisone, Gilberto / Dodt, Hans-Ulrich / Hökfelt, Tomas / Harkany, Tibor / Romanov, Roman A

Nature communications

2022 Volume 13, Issue 1, Page(s) 5944

Abstract: The lateral septum (LS) has been implicated in the regulation of locomotion. Nevertheless, the neurons synchronizing LS activity with the brain's clock in the suprachiasmatic nucleus (SCN) remain unknown. By interrogating the molecular, anatomical and ... ...

Abstract	The lateral septum (LS) has been implicated in the regulation of locomotion. Nevertheless, the neurons synchronizing LS activity with the brain's clock in the suprachiasmatic nucleus (SCN) remain unknown. By interrogating the molecular, anatomical and physiological heterogeneity of dopamine neurons of the periventricular nucleus (PeVN; A14 catecholaminergic group), we find that Th
MeSH term(s)	Animals ; Dopamine/physiology ; Hypothalamus ; Mice ; Neurons/physiology ; Somatostatin ; Suprachiasmatic Nucleus/physiology
Chemical Substances	Somatostatin (51110-01-1) ; Dopamine (VTD58H1Z2X)
Language	English
Publishing date	2022-10-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-33584-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Visualizing minute details in light-sheet and confocal microscopy data by combining 3D rolling ball filtering and deconvolution.

Becker, Klaus / Saghafi, Saiedeh / Pende, Marko / Hahn, Christian / Dodt, Hans Ulrich

Journal of biophotonics

2021 Volume 15, Issue 2, Page(s) e202100290

Abstract: We developed an open-source deconvolution software that stunningly increases the visibility of minute details, as for example, neurons or nerve fibers in light-sheet microscopy or confocal microscopy data by combining rolling ball background subtraction ... ...

Abstract	We developed an open-source deconvolution software that stunningly increases the visibility of minute details, as for example, neurons or nerve fibers in light-sheet microscopy or confocal microscopy data by combining rolling ball background subtraction in three directions with deconvolution using a synthetic or measured point spread function. Via automatic block-wise processing image stacks of virtually unlimited size can be deconvolved even on small computers with 8 or 16 GB RAM. By parallelization and optional GPU-acceleration, the software works with high speed: On a PC equipped with a state-of-the-art NVidia graphic board a three dimensional (3D)-stack of about 1 billion voxels can be deconvolved within 5 to 10 minutes. The implemented variation of the Richardson-Lucy deconvolution algorithm preserves the photogrammetry of the image data by using flux-preserving regularization, an approach that to our knowledge has not been applied for deconvolving microscopy data before.
MeSH term(s)	Acceleration ; Algorithms ; Microscopy, Confocal/methods ; Neurons ; Software
Language	English
Publishing date	2021-11-17
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2390063-5
ISSN	1864-0648 ; 1864-063X
ISSN (online)	1864-0648
ISSN	1864-063X
DOI	10.1002/jbio.202100290
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Article ; Online: Deconvolution of light sheet microscopy recordings

Klaus Becker / Saiedeh Saghafi / Marko Pende / Inna Sabdyusheva-Litschauer / Christian M. Hahn / Massih Foroughipour / Nina Jährling / Hans-Ulrich Dodt

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 14

Abstract: Abstract We developed a deconvolution software for light sheet microscopy that uses a theoretical point spread function, which we derived from a model of image formation in a light sheet microscope. We show that this approach provides excellent blur ... ...

Abstract	Abstract We developed a deconvolution software for light sheet microscopy that uses a theoretical point spread function, which we derived from a model of image formation in a light sheet microscope. We show that this approach provides excellent blur reduction and enhancement of fine image details for image stacks recorded with low magnification objectives of relatively high NA and high field numbers as e.g. 2x NA 0.14 FN 22, or 4x NA 0.28 FN 22. For these objectives, which are widely used in light sheet microscopy, sufficiently resolved point spread functions that are suitable for deconvolution are difficult to measure and the results obtained by common deconvolution software developed for confocal microscopy are usually poor. We demonstrate that the deconvolutions computed using our point spread function model are equivalent to those obtained using a measured point spread function for a 10x objective with NA 0.3 and for a 20x objective with NA 0.45.
Keywords	Medicine ; R ; Science ; Q
Subject code	535
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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