scholarly journals Cerebellar contributions to a brainwide network for flexible behavior

2021 ◽  
Author(s):  
Jessica L Verpeut ◽  
Silke Bergeler ◽  
Mikhail Kislin ◽  
F William Townes ◽  
Ugne Klibaite ◽  
...  
Keyword(s):  
Open Field ◽  
Body Movement ◽  
Automated Analysis ◽  
Light Sheet ◽  
Anterior Cingulate ◽  
Whole Body ◽  
Light Sheet Microscopy ◽  
Field Environment ◽  
Flexible Behavior ◽  
Crus I

The cerebellum regulates nonmotor behavior, but the routes by which it exerts its influence are not well characterized. Here we report a necessary role for posterior cerebellum in guiding flexible behavior, acting through a network of diencephalic and neocortical structures. After chemogenetic inhibition of Purkinje cells in lobule VI or crus I, high-throughput automated analysis of complex whole-body movement revealed deficiencies in adaptation across days to an open field environment. Neither perturbation affected gait, within-day open-field adaptation, or location preference. In a Y-maze task, mice could learn but were impaired in their ability to reverse their initial choice. To map targets of perturbation, we imaged c-Fos activation in cleared whole brains using light-sheet microscopy. Reversal learning activated diencephalic regions and associative neocortical regions. Distinctive subsets of structures were altered by perturbation of lobule VI (thalamus and habenula) and crus I (hypothalamus and prelimbic/orbital cortex), and both perturbations influenced anterior cingulate and infralimbic cortex. Taken together, these experiments reveal parts of a brainwide system for cerebellar influence to guide flexible learning.

scholarly journals Wide field light-sheet microscopy with lens-axicon controlled two-photon Bessel beam illumination

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sota Takanezawa ◽  
Takashi Saitou ◽  
Takeshi Imamura
Keyword(s):  
High Speed ◽  
Bessel Beam ◽  
Light Sheet ◽  
Time Lapse ◽  
Whole Body ◽  
Wide Field ◽  
Two Photon ◽  
Light Sheet Microscopy ◽  
Photon Excitation ◽  
Two Photon Excitation

AbstractTwo-photon excitation can lower phototoxicity and improve penetration depth, but its narrow excitation range restricts its applications in light-sheet microscopy. Here, we propose simple illumination optics, a lens-axicon triplet composed of an axicon and two convex lenses, to generate longer extent Bessel beams. This unit can stretch the beam full width at half maximum of 600–1000 μm with less than a 4-μm waist when using a 10× illumination lens. A two-photon excitation digital scanned light-sheet microscope possessing this range of field of view and ~2–3-μm axial resolution is constructed and used to analyze the cellular dynamics over the whole body of medaka fish. We demonstrate long-term time-lapse observations over several days and high-speed recording with ~3 mm3 volume per 4 s of the embryos. Our system is minimal and suppresses laser power loss, which can broaden applications of two-photon excitation in light-sheet microscopy.

scholarly journals Cell morphological motif detector for high-resolution 3D microscopy images

2018 ◽  
Author(s):  
Meghan K. Driscoll ◽  
Erik S. Welf ◽  
Kevin M. Dean ◽  
Reto Fiolka ◽  
Gaudenz Danuser
Keyword(s):  
Intracellular Signaling ◽  
Molecular Mechanisms ◽  
Automated Analysis ◽  
Light Sheet ◽  
Cell Types ◽  
Light Sheet Microscopy ◽  
Cytoskeletal Dynamics ◽  
Computational Workflow ◽  
Analytical Tools ◽  
Microscopy Images

AbstractRecent advances in light-sheet microscopy enable imaging of cell morphology and signaling with unprecedented detail. However, the analytical tools to systematically measure and visualize the intricate relations between cell morphodynamics, intracellular signaling, and cytoskeletal dynamics have been largely missing. Here, we introduce a set of computer vision and graphics methods to dissect molecular mechanisms underlying 3D cell morphogenesis and to test whether morphogenesis itself affects intracellular signaling. We demonstrate a machine learning based generic morphological motif detector that automatically finds lamellipodia, filopodia, and blebs on various cell types. Combining motif detection with molecular localization, we measure the differential association of PIP2 and KrasV12 with blebs. Both signals associate with bleb edges, as expected for membrane-localized proteins, but only PIP2 is enhanced on blebs. This suggests that local morphological cues differentially organize and activate sub-cellular signaling processes. Overall, our computational workflow enables the objective, automated analysis of the 3D coupling of morphodynamics with cytoskeletal dynamics and intracellular signaling.

scholarly journals Parallel organization of cerebellar pathways to sensorimotor, associative, and modulatory forebrain

2020 ◽  
Author(s):  
Thomas J. Pisano ◽  
Zahra M. Dhanerawala ◽  
Mikhail Kislin ◽  
Dariya Bakshinskaya ◽  
Esteban A. Engel ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Light Sheet ◽  
Anterior Cingulate ◽  
Thalamic Nuclei ◽  
Light Sheet Microscopy ◽  
Ascending Pathways ◽  
Motor Information ◽  
Lateral Posterior ◽  
Simplex Virus

AbstractCerebellar outputs take almost exclusively polysynaptic routes to reach the rest of the brain, impeding conventional tracing efforts. Here we quantify pathways between cerebellar cortex and contralateral thalamic and corticostriatal structures using an anterograde (H129) transsynaptic tracer herpes simplex virus type 1, a retrograde (Bartha) tracer pseudorabies virus, and a whole-brain pipeline for neuron-level analysis using light-sheet microscopy. In ascending pathways, sensorimotor regions contained the most labeled neurons, but higher densities were found in associative areas, including orbital, anterior cingulate, prelimbic, and infralimbic cortex. Ascending paths passed through most thalamic nuclei, especially ventral posteromedial and lateral posterior (sensorimotor), mediodorsal (associative), and reticular (modulatory) nuclei. Retrograde tracing revealed that the majority of descending paths originate from somatomotor cortex. Patterns of ascending influence correlated with anatomical pathway strengths, as measured by brainwide mapping of c-Fos responses to optogenetic inhibition of Purkinje cells. Our results reveal parallel functional networks linking cerebellum to forebrain and suggest that cerebellum is capable of using sensory-motor information to guide both movement and nonmotor functions.

scholarly journals Combining Deep Learning and Active Contours Opens The Way to Robust, Automated Analysis of Brain Cytoarchitectonics

2018 ◽  
Author(s):  
Konstantin Thierbach ◽  
Pierre-Louis Bazin ◽  
Walter De Back ◽  
Filippos Gavriilidis ◽  
Evgeniya Kirilina ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Active Contours ◽  
Feedforward Neural Networks ◽  
Automated Analysis ◽  
Light Sheet ◽  
Cell Detection ◽  
Light Sheet Microscopy ◽  
And Topology ◽  
High Level

AbstractDeep learning has thoroughly changed the field of image analysis yielding impressive results whenever enough annotated data can be gathered. While partial annotation can be very fast, manual segmentation of 3D biological structures is tedious and error-prone. Additionally, high-level shape concepts such as topology or boundary smoothness are hard if not impossible to encode in Feedforward Neural Networks. Here we present a modular strategy for the accurate segmentation of neural cell bodies from light-sheet microscopy combining mixed-scale convolutional neural networks and topology-preserving geometric deformable models. We show that the network can be trained efficiently from simple cell centroid annotations, and that the final segmentation provides accurate cell detection and smooth segmentations that do not introduce further cell splitting or merging.

scholarly journals Elimination of fibrin γ-chain cross-linking by FXIIIa increases pulmonary embolism arising from murine inferior vena cava thrombi

2021 ◽  
Vol 118 (27) ◽  
pp. e2103226118
Author(s):  
Cédric Duval ◽  
Adomas Baranauskas ◽  
Tímea Feller ◽  
Majid Ali ◽  
Lih T. Cheah ◽  
...  
Keyword(s):  
Pulmonary Embolism ◽  
Factor Xiii ◽  
Treatment Options ◽  
Vena Cava ◽  
Light Sheet ◽  
Whole Body ◽  
Cross Linking ◽  
Light Sheet Microscopy ◽  
Clot Stability

The onset of venous thromboembolism, including pulmonary embolism, represents a significant health burden affecting more than 1 million people annually worldwide. Current treatment options are based on anticoagulation, which is suboptimal for preventing further embolic events. In order to develop better treatments for thromboembolism, we sought to understand the structural and mechanical properties of blood clots and how this influences embolism in vivo. We developed a murine model in which fibrin γ-chain cross-linking by activated Factor XIII is eliminated (FGG3X) and applied methods to study thromboembolism at whole-body and organ levels. We show that FGG3X mice have a normal phenotype, with overall coagulation parameters and platelet aggregation and function largely unaffected, except for total inhibition of fibrin γ-chain cross-linking. Elimination of fibrin γ-chain cross-linking resulted in thrombi with reduced strength that were prone to fragmentation. Analysis of embolism in vivo using Xtreme optical imaging and light sheet microscopy demonstrated that the elimination of fibrin γ-chain cross-linking resulted in increased embolization without affecting clot size or lysis. Our findings point to a central previously unrecognized role for fibrin γ-chain cross-linking in clot stability. They also indirectly indicate mechanistic targets for the prevention of thrombosis through selective modulation of fibrin α-chain but not γ-chain cross-linking by activated Factor XIII to reduce thrombus size and burden, while maintaining clot stability and preventing embolism.

scholarly journals Achromatic terahertz Airy beam generation with dielectric metasurfaces

Nanophotonics ◽  
2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Qingqing Cheng ◽  
Juncheng Wang ◽  
Ling Ma ◽  
Zhixiong Shen ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Biomedical Imaging ◽  
Frequency Dispersion ◽  
Light Sheet ◽  
Photonic Devices ◽  
Self Healing ◽  
Beam Focusing ◽  
Light Sheet Microscopy ◽  
Airy Beam ◽  
Potential Applications ◽  
Airy Beams

AbstractAiry beams exhibit intriguing properties such as nonspreading, self-bending, and self-healing and have attracted considerable recent interest because of their many potential applications in photonics, such as to beam focusing, light-sheet microscopy, and biomedical imaging. However, previous approaches to generate Airy beams using photonic structures have suffered from severe chromatic problems arising from strong frequency dispersion of the scatterers. Here, we design and fabricate a metasurface composed of silicon posts for the frequency range 0.4–0.8 THz in transmission mode, and we experimentally demonstrate achromatic Airy beams exhibiting autofocusing properties. We further show numerically that a generated achromatic Airy-beam-based metalens exhibits self-healing properties that are immune to scattering by particles and that it also possesses a larger depth of focus than a traditional metalens. Our results pave the way to the realization of flat photonic devices for applications to noninvasive biomedical imaging and light-sheet microscopy, and we provide a numerical demonstration of a device protocol.

scholarly journals Single-Molecule Light-Sheet Microscopy with Local Nanopipette Delivery

2021 ◽  
Vol 93 (8) ◽  
pp. 4092-4099
Author(s):  
Bing Li ◽  
Aleks Ponjavic ◽  
Wei-Hsin Chen ◽  
Lee Hopkins ◽  
Craig Hughes ◽  
...  
Keyword(s):  
Single Molecule ◽  
Light Sheet ◽  
Light Sheet Microscopy

scholarly journals Effect of captopril on post-infarction remodelling visualized by light sheet microscopy and echocardiography

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Urmas Roostalu ◽  
Louise Thisted ◽  
Jacob Lercke Skytte ◽  
Casper Gravesen Salinas ◽  
Philip Juhl Pedersen ◽  
...  
Keyword(s):  
Morphological Changes ◽  
Light Sheet ◽  
Automated Image Analysis ◽  
Border Zone ◽  
Vascular Density ◽  
Mouse Heart ◽  
Imaging Method ◽  
Light Sheet Microscopy ◽  
Post Surgery ◽  
Captopril Treatment

AbstractAngiotensin converting enzyme inhibitors, among them captopril, improve survival following myocardial infarction (MI). The mechanisms of captopril action remain inadequately understood due to its diverse effects on multiple signalling pathways at different time periods following MI. Here we aimed to establish the role of captopril in late-stage post-MI remodelling. Left anterior descending artery (LAD) ligation or sham surgery was carried out in male C57BL/6J mice. Seven days post-surgery LAD ligated mice were allocated to daily vehicle or captopril treatment continued over four weeks. To provide comprehensive characterization of the changes in mouse heart following MI a 3D light sheet imaging method was established together with automated image analysis workflow. The combination of echocardiography and light sheet imaging enabled to assess cardiac function and the underlying morphological changes. We show that delayed captopril treatment does not affect infarct size but prevents left ventricle dilation and hypertrophy, resulting in improved ejection fraction. Quantification of lectin perfused blood vessels showed improved vascular density in the infarct border zone in captopril treated mice in comparison to vehicle dosed control mice. These results validate the applicability of combined echocardiographic and light sheet assessment of drug mode of action in preclinical cardiovascular research.

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