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  1. Article: Guide to the construction and use of an adaptive optics two-photon microscope with direct wavefront sensing.

    Yao, Pantong / Liu, Rui / Broginni, Thomas / Thunemann, Martin / Kleinfeld, David

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Two-photon microscopy, combined with appropriate optical labeling, has enabled the study of structure and function throughout nervous systems. This methodology enables, for example, the measurement and tracking of sub-micrometer structures within brain ... ...

    Abstract Two-photon microscopy, combined with appropriate optical labeling, has enabled the study of structure and function throughout nervous systems. This methodology enables, for example, the measurement and tracking of sub-micrometer structures within brain cells, the spatio-temporal mapping of spikes in individual neurons, and the spatio-temporal mapping of transmitter release in individual synapses. Yet the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300 to 400 µm of neocortex. To obviate this limitation, we measure the wavefront at the focus of the excitation beam and utilize adaptive optics that alters the incident wavefront to achieve an improved focal volume. We describe the constructions, calibration, and operation of a two-photon microscopy that incorporates adaptive optics to restore diffraction-limited resolution throughout the nearly 900 µm depth of mouse cortex. Our realization utilizes a guide star formed by excitation of red-shifted dye within the blood serum to directly measure the wavefront. We incorporate predominantly commercial optical, optomechanical, mechanical, and electronic components; computer aided design models of the exceptional custom components are supplied. The design is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in mouse neocortex by imaging the morphology of somatostatin-expressing neurons at 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons, and glutamate transmission to L4 neurons.
    Language English
    Publishing date 2023-01-24
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.24.525307
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing.

    Yao, Pantong / Liu, Rui / Broggini, Thomas / Thunemann, Martin / Kleinfeld, David

    Nature protocols

    2023  Volume 18, Issue 12, Page(s) 3732–3766

    Abstract: Two-photon microscopy, combined with the appropriate optical labelling, enables the measurement and tracking of submicrometer structures within brain cells, as well as the spatiotemporal mapping of spikes in individual neurons and of neurotransmitter ... ...

    Abstract Two-photon microscopy, combined with the appropriate optical labelling, enables the measurement and tracking of submicrometer structures within brain cells, as well as the spatiotemporal mapping of spikes in individual neurons and of neurotransmitter release in individual synapses. Yet, the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths of more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300-400 µm of the neocortex. To obviate this limitation, we shape the focal volume, generated by the excitation beam, by modulating the incident wavefront via guidestar-assisted adaptive optics. Here, we describe the construction, calibration and operation of a two-photon microscope that incorporates adaptive optics to restore diffraction-limited resolution at depths close to 900 µm in the mouse cortex. Our setup detects a guidestar formed by the excitation of a red-shifted dye in blood serum, used to directly measure the wavefront. We incorporate predominantly commercially available optical, optomechanical, mechanical and electronic components, and supply computer-aided design models of other customized components. The resulting adaptive optics two-photon microscope is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in the mouse neocortex by imaging the morphology of somatostatin-expressing neurons that lie 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons and thalamocortical glutamate transmission to L4 neurons. The protocol requires ~30 d to complete and is suitable for users with graduate-level expertise in optics.
    MeSH term(s) Mice ; Animals ; Microscopy ; Optics and Photonics ; Photons ; Neurons ; Calcium
    Chemical Substances Calcium (SY7Q814VUP)
    Language English
    Publishing date 2023-11-01
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-023-00893-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Impact of Brain Surface Boundary Conditions on Electrophysiology and Implications for Electrocorticography.

    Rogers, Nicholas / Thunemann, Martin / Devor, Anna / Gilja, Vikash

    Frontiers in neuroscience

    2020  Volume 14, Page(s) 763

    Abstract: Volume conduction of electrical potentials in the brain is highly influenced by the material properties and geometry of the tissue and recording devices implanted into the tissue. These effects are very large in EEG due to the volume conduction through ... ...

    Abstract Volume conduction of electrical potentials in the brain is highly influenced by the material properties and geometry of the tissue and recording devices implanted into the tissue. These effects are very large in EEG due to the volume conduction through the skull and scalp but are often neglected in intracranial electrophysiology. When considering penetrating electrodes deep in the brain, the assumption of an infinite and homogenous medium can be used when the sources are far enough from the brain surface and the electrodes to minimize the boundary effect. When the electrodes are recording from the brain's surface the effect of the boundary cannot be neglected, and the large surface area and commonly used insulating materials in surface electrode arrays may further increase the effect by altering the nature of the boundary in the immediate vicinity of the electrodes. This gives the experimenter some control over the spatial profiles of the potentials by appropriate design of the electrode arrays. We construct a simple three-layer model to describe the effect of material properties and geometry above the brain surface on the electric potentials and conduct empirical experiments to validate this model. A laminar electrode array is used to measure the effect of insulating and relatively conducting layers above the cortical surface by recording evoked potentials alternating between a dried surface and saline covering layer, respectively. Empirically, we find that an insulating boundary amplifies the potentials relative to conductive saline by about a factor of 4, and that the effect is not constrained to potentials that originate near the surface. The model is applied to predict the influence of array design and implantation procedure on the recording amplitude and spatial selectivity of the surface electrode arrays.
    Language English
    Publishing date 2020-08-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2411902-7
    ISSN 1662-453X ; 1662-4548
    ISSN (online) 1662-453X
    ISSN 1662-4548
    DOI 10.3389/fnins.2020.00763
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Tissue Oxygen Depth Explorer: an interactive database for microscopic oxygen imaging data.

    Amra, Layth N / Mächler, Philipp / Fomin-Thunemann, Natalie / Kılıç, Kıvılcım / Saisan, Payam / Devor, Anna / Thunemann, Martin

    Frontiers in neuroinformatics

    2023  Volume 17, Page(s) 1278787

    Language English
    Publishing date 2023-11-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2452979-5
    ISSN 1662-5196
    ISSN 1662-5196
    DOI 10.3389/fninf.2023.1278787
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: PV interneurons evoke astrocytic Ca

    Krogsgaard, Aske / Sperling, Leonora / Dahlqvist, Matilda / Thomsen, Kirsten / Vydmantaite, Gabriele / Li, Fangyuan / Thunemann, Martin / Lauritzen, Martin / Lind, Barbara Lykke

    Glia

    2023  Volume 71, Issue 8, Page(s) 1830–1846

    Abstract: Neurovascular coupling (NVC) modulates cerebral blood flow to match increased metabolic demand during neuronal excitation. Activation of inhibitory interneurons also increase blood flow, but the basis for NVC caused by interneurons is unclear. While ... ...

    Abstract Neurovascular coupling (NVC) modulates cerebral blood flow to match increased metabolic demand during neuronal excitation. Activation of inhibitory interneurons also increase blood flow, but the basis for NVC caused by interneurons is unclear. While astrocyte Ca
    MeSH term(s) Mice ; Animals ; Neurovascular Coupling/physiology ; Astrocytes/metabolism ; Wakefulness ; Cerebrovascular Circulation/physiology ; Interneurons
    Language English
    Publishing date 2023-03-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639414-0
    ISSN 1098-1136 ; 0894-1491
    ISSN (online) 1098-1136
    ISSN 0894-1491
    DOI 10.1002/glia.24370
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Time-Lagged Functional Ultrasound for Multi-Parametric Cerebral Hemodynamic Imaging.

    Liu, Bingxue / Wang, Yongchao / Fomin-Thunemann, Natalie / Thunemann, Martin / Kilic, Kivilcim / Devor, Anna / Cheng, Xiaojun / Tan, Jiyong / Jiang, John / Boas, David A / Tang, Jianbo

    IEEE transactions on medical imaging

    2024  Volume 43, Issue 2, Page(s) 638–648

    Abstract: We introduce an ultrasound speckle decorrelation-based time-lagged functional ultrasound technique (tl-fUS) for the quantification of the relative changes in cerebral blood flow speed (rCBF [Formula: see text]), cerebral blood volume (rCBV) and cerebral ... ...

    Abstract We introduce an ultrasound speckle decorrelation-based time-lagged functional ultrasound technique (tl-fUS) for the quantification of the relative changes in cerebral blood flow speed (rCBF [Formula: see text]), cerebral blood volume (rCBV) and cerebral blood flow (rCBF) during functional stimulations. Numerical simulations, phantom validations, and in vivo mouse brain experiments were performed to test the capability of tl-fUS to parse out and quantify the ratio change of these hemodynamic parameters. The blood volume change was found to be more prominent in arterioles compared to venules and the peak blood flow changes were around 2.5 times the peak blood volume change during brain activation, agreeing with previous observations in the literature. The tl-fUS shows the ability of distinguishing the relative changes of rCBFspeed, rCBV, and rCBF, which can inform specific physiological interpretations of the fUS measurements.
    MeSH term(s) Animals ; Mice ; Hemodynamics ; Blood Volume ; Brain Neoplasms ; Ultrasonography ; Brain/diagnostic imaging ; Cerebrovascular Circulation ; Magnetic Resonance Imaging/methods
    Language English
    Publishing date 2024-02-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 622531-7
    ISSN 1558-254X ; 0278-0062
    ISSN (online) 1558-254X
    ISSN 0278-0062
    DOI 10.1109/TMI.2023.3314734
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  7. Article: Visual stimulation drives retinotopic acetylcholine release in the mouse visual cortex.

    Knudstrup, Scott G / Martinez, Catalina / Rauscher, Bradley C / Doran, Patrick R / Fomin-Thunemann, Natalie / Kilic, Kivilcim / Jiang, John / Devor, Anna / Thunemann, Martin / Gavornik, Jeffrey P

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Cholinergic signaling is involved with a variety of brain functions including learning and memory, attention, and behavioral state modulation. The spatiotemporal characteristics of neocortical acetylcholine (ACh) release in response to sensory inputs are ...

    Abstract Cholinergic signaling is involved with a variety of brain functions including learning and memory, attention, and behavioral state modulation. The spatiotemporal characteristics of neocortical acetylcholine (ACh) release in response to sensory inputs are poorly understood, but a lack of intra-region topographic organization of cholinergic projections from the basal forebrain has suggested diffuse release patterns and volume transmission. Here, we use mesoscopic imaging of fluorescent ACh sensors to show that visual stimulation results in ACh release patterns that conform to a retinotopic map of visual space in the mouse primary visual cortex, suggesting new modes of functional cholinergic signaling in cortical circuits.x.
    Language English
    Publishing date 2024-02-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.04.578821
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Protocol to visualize CD11c

    Sauter, Manuela / Sauter, Reinhard J / Olbrich, Marcus / Thunemann, Martin / Feil, Susanne / Feil, Robert / Langer, Harald F

    STAR protocols

    2022  Volume 3, Issue 3, Page(s) 101645

    Abstract: Here, we describe ... ...

    Abstract Here, we describe an
    MeSH term(s) Animals ; Atherosclerosis/genetics ; CD11c Antigen/genetics ; Lac Operon/genetics ; Mice ; Mice, Knockout ; Plaque, Atherosclerotic/genetics
    Chemical Substances CD11c Antigen
    Language English
    Publishing date 2022-08-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.101645
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  9. Article: Widefield in vivo imaging system with two fluorescence and two reflectance channels, a single sCMOS detector, and shielded illumination.

    Doran, Patrick R / Fomin-Thunemann, Natalie / Tang, Rockwell P / Balog, Dora / Zimmerman, Bernhard / Kilic, Kivilcim / Martin, Emily A / Kura, Sreekanth / Fisher, Harrison P / Chabbott, Grace / Herbert, Joel / Rauscher, Bradley C / Jiang, John X / Sakadzic, Sava / Boas, David A / Devor, Anna / Chen, Ichun Anderson / Thunemann, Martin

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Significance: Widefield microscopy of the entire dorsal part of mouse cerebral cortex enables large-scale (mesoscopic) imaging of neuronal activity with fluorescent indicators as well as hemodynamics via oxy- and deoxyhemoglobin absorption. Versatile ... ...

    Abstract Significance: Widefield microscopy of the entire dorsal part of mouse cerebral cortex enables large-scale (mesoscopic) imaging of neuronal activity with fluorescent indicators as well as hemodynamics via oxy- and deoxyhemoglobin absorption. Versatile and cost-effective imaging systems are needed for large-scale, color-multiplexed imaging of multiple fluorescent and intrinsic contrasts.
    Aim: Develop a system for mesoscopic imaging of two fluorescent and two reflectance channels.
    Approach: Excitation of red and green fluorescence is achieved through epi-illumination. Hemoglobin absorption imaging is achieved using 525- and 625nm LEDs positioned around the objective lens. An aluminum hemisphere placed between objective and cranial window provides diffuse illumination of the brain. Signals are recorded sequentially by a single sCMOS detector.
    Results: We demonstrate performance of our imaging system by recording large-scale spontaneous and stimulus-evoked neuronal, cholinergic, and hemodynamic activity in awake head-fixed mice with a curved crystal skull window expressing the red calcium indicator jRGECO1a and the green acetylcholine sensor GRABACh3.0 . Shielding of illumination light through the aluminum hemisphere enables concurrent recording of pupil diameter changes.
    Conclusions: Our widefield microscope design with single camera can be used to acquire multiple aspects of brain physiology and is compatible with behavioral readouts of pupil diameter.
    Language English
    Publishing date 2024-03-13
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.07.566086
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  10. Article: Chronic Cranial Windows for Long Term Multimodal Neurovascular Imaging in Mice.

    Kılıç, Kıvılcım / Desjardins, Michèle / Tang, Jianbo / Thunemann, Martin / Sunil, Smrithi / Erdener, Şefik Evren / Postnov, Dmitry D / Boas, David A / Devor, Anna

    Frontiers in physiology

    2021  Volume 11, Page(s) 612678

    Abstract: Chronic cranial windows allow for longitudinal brain imaging experiments in awake, behaving mice. Different imaging technologies have their unique advantages and combining multiple imaging modalities offers measurements of a wide spectrum of neuronal, ... ...

    Abstract Chronic cranial windows allow for longitudinal brain imaging experiments in awake, behaving mice. Different imaging technologies have their unique advantages and combining multiple imaging modalities offers measurements of a wide spectrum of neuronal, glial, vascular, and metabolic parameters needed for comprehensive investigation of physiological and pathophysiological mechanisms. Here, we detail a suite of surgical techniques for installation of different cranial windows targeted for specific imaging technologies and their combination. Following these techniques and practices will yield higher experimental success and reproducibility of results.
    Language English
    Publishing date 2021-01-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564217-0
    ISSN 1664-042X
    ISSN 1664-042X
    DOI 10.3389/fphys.2020.612678
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