Multiphoton intravital microscopy in small animals: motion artefact challenges and technical solutions

Functional imaging of visual cortical layers and subplate in awake mice with optimized three-photon microscopy

(2019) Murat Yildirim et al.   Nature Communications

Longitudinal study of hemodynamics and dendritic membrane potential changes in the mouse cortex following a soft cranial window installation

(2019) Hyejin Park et al.   Neurophotonics

Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models

(2019) Mohammad Haft-Javaherian et al.   PLoS One

Confocal and multiphoton calcium imaging of the enteric nervous system in anesthetized mice

(2019) Yuki Motegi et al.   NEUROSCIENCE RESEARCH

Fast and robust active neuron segmentation in two-photon calcium imaging using spatiotemporal deep learning

(2019) Somayyeh Soltanian-Zadeh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Imaging in vivo dynamics of sensory axon responses to CNS injury

(2019) Barbara Schaffran et al.   EXPERIMENTAL NEUROLOGY

Imaging spinal cord activity in behaving animals

(2019) Nicholas A. Nelson et al.   EXPERIMENTAL NEUROLOGY

In vivo imaging of the pathophysiological changes and neutrophil dynamics in influenza virus-infected mouse lungs

(2018) Hiroshi Ueki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chronic 2P-STED imaging reveals high turnover of dendritic spines in the hippocampus in vivo

(2018) Thomas Pfeiffer et al.   eLife

Intravital imaging with two-photon microscopy reveals cellular dynamics in the ischeamia-reperfused rat heart

(2018) Ryohei Matsuura et al.   Scientific Reports

In Vivo Calcium Imaging of Cardiomyocytes in the Beating Mouse Heart With Multiphoton Microscopy

(2018) Jason S. Jones et al.   Frontiers in Physiology

Laser speckle contrast imaging of blood flow in the deep brain using microendoscopy

(2018) Ming Chen et al.   OPTICS LETTERS

Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)

(2017) Alexander Song et al.   NATURE METHODS

Fast high-resolution miniature two-photon microscopy for brain imaging in freely behaving mice

(2017) Weijian Zong et al.   NATURE METHODS

Particle Tracking Facilitates Real Time Capable Motion Correction in 2D or 3D Two-Photon Imaging of Neuronal Activity

(2017) Samira Aghayee et al.   Frontiers in Neural Circuits

Fast varifocal two-photon microendoscope for imaging neuronal activity in the deep brain

(2017) Masaaki Sato et al.   Biomedical Optics Express

A Novel Cervical Spinal Cord Window Preparation Allows for Two-Photon Imaging of T-Cell Interactions with the Cervical Spinal Cord Microvasculature during Experimental Autoimmune Encephalomyelitis

(2017) Neda Haghayegh Jahromi et al.   Frontiers in Immunology

Intubation-free in vivo imaging of the tracheal mucosa using two-photon microscopy

(2017) Tibor Z. Veres et al.   Scientific Reports

Allergen-Induced CD4+T Cell Cytokine Production within Airway Mucosal Dendritic Cell–T Cell Clusters Drives the Local Recruitment of Myeloid Effector Cells

(2016) Tibor Z. Veres et al.   JOURNAL OF IMMUNOLOGY

A survey of medical image registration – under review

(2016) Max A. Viergever et al.   MEDICAL IMAGE ANALYSIS

Random-access scanning microscopy for 3D imaging in awake behaving animals

(2016) K M Naga Srinivas Nadella et al.   NATURE METHODS

Imaging large-scale cellular activity in spinal cord of freely behaving mice

(2016) Kohei J. Sekiguchi et al.   Nature Communications

Automated frame selection process for high-resolution microendoscopy

(2015) Ayumu Ishijima et al.   JOURNAL OF BIOMEDICAL OPTICS

Imaging liver biology in vivo using conventional confocal microscopy

(2015) Pedro E Marques et al.   Nature Protocols

Automatic Morphological Reconstruction of Neurons from Multiphoton and Confocal Microscopy Images Using 3D Tubular Models

(2015) Alberto Santamaría-Pang et al.   NEUROINFORMATICS

In vivo imaging reveals PKA regulation of ERK activity during neutrophil recruitment to inflamed intestines

(2014) Rei Mizuno et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Neutrophils Mediate Blood–Spinal Cord Barrier Disruption in Demyelinating Neuroinflammatory Diseases

(2014) Benoit Aubé et al.   JOURNAL OF IMMUNOLOGY

Motion compensation for in vivo subcellular optical microscopy

(2014) B. LUCOTTE et al.   JOURNAL OF MICROSCOPY

Long-Term In Vivo Imaging of Dendritic Spines in the Hippocampus Reveals Structural Plasticity

(2014) L. Gu et al.   JOURNAL OF NEUROSCIENCE

Voltage Imaging of Waking Mouse Cortex Reveals Emergence of Critical Neuronal Dynamics

(2014) G. Scott et al.   JOURNAL OF NEUROSCIENCE

Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging

(2014) Laila Ritsma et al.   NATURE

Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo

(2014) Adam M Packer et al.   NATURE METHODS

Visualizing mammalian brain area interactions by dual-axis two-photon calcium imaging

(2014) Jérôme Lecoq et al.   NATURE NEUROSCIENCE

High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor

(2014) François St-Pierre et al.   NATURE NEUROSCIENCE

Zolpidem Reduces Hippocampal Neuronal Activity in Freely Behaving Mice: A Large Scale Calcium Imaging Study with Miniaturized Fluorescence Microscope

(2014) Tamara Berdyyeva et al.   PLoS One

Intravital imaging of cardiac function at the single-cell level

(2014) A. D. Aguirre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated motion artifact removal for intravital microscopy, without a priori information

(2014) Sungon Lee et al.   Scientific Reports

SIMA: Python software for analysis of dynamic fluorescence imaging data

(2014) Patrick Kaifosh et al.   Frontiers in Neuroinformatics

Two-Photon Excitation STED Microscopy in Two Colors in Acute Brain Slices

(2013) Philipp Bethge et al.   BIOPHYSICAL JOURNAL

High-Resolution Imaging of Intravascular Atherogenic Inflammation in Live Mice

(2013) Raphael Chèvre et al.   CIRCULATION RESEARCH

Advanced Motion Compensation Methods for Intravital Optical Microscopy

(2013) Claudio Vinegoni et al.   IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS

Two-Photon Intravital Imaging of Lungs during Anthrax Infection Reveals Long-Lasting Macrophage-Dendritic Cell Contacts

(2013) Daniel Fiole et al.   INFECTION AND IMMUNITY

Nonlinear motion compensation using cubature Kalman filter forin vivofluorescence microendoscopy in peripheral lung cancer intervention

(2013) Tiancheng He et al.   JOURNAL OF BIOMEDICAL OPTICS

Two-Photon Processor and SeNeCA: a freely available software package to process data from two-photon calcium imaging at speeds down to several milliseconds per frame

(2013) Jakub Tomek et al.   JOURNAL OF NEUROPHYSIOLOGY

Long- and short-term intravital imaging reveals differential spatiotemporal recruitment and function of myelomonocytic cells after spinal cord injury

(2013) Keith K. Fenrich et al.   JOURNAL OF PHYSIOLOGY-LONDON

A Motion Correction Framework for Time Series Sequences in Microscopy Images

(2013) Ankur N. Kumar et al.   MICROSCOPY AND MICROANALYSIS

Long-term dynamics of CA1 hippocampal place codes

(2013) Yaniv Ziv et al.   NATURE NEUROSCIENCE

In Vivo Imaging of Enteric Neurogenesis in the Deep Tissue of Mouse Small Intestine

(2013) Kei Goto et al.   PLoS One

A Spinal Cord Window Chamber Model for In Vivo Longitudinal Multimodal Optical and Acoustic Imaging in a Murine Model

(2013) Sarah A. Figley et al.   PLoS One

Automated Filtering of Intrinsic Movement Artifacts during Two-Photon Intravital Microscopy

(2013) Denis Soulet et al.   PLoS One

Optical pacing of the adult rabbit heart

(2013) Michael W. Jenkins et al.   Biomedical Optics Express

Functional imaging in freely moving animals

(2012) Jason ND Kerr et al.   CURRENT OPINION IN NEUROBIOLOGY

Complex morphology and functional dynamics of vital murine intestinal mucosa revealed by autofluorescence 2-photon microscopy

(2012) Antje Klinger et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Intravital 2-photon imaging of leukocyte trafficking in beating heart

(2012) Wenjun Li et al.   JOURNAL OF CLINICAL INVESTIGATION

Visualization of mucosal homeostasis via single- and multiphoton intravital fluorescence microscopy

(2012) C. Xu et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Three-dimensional motion tracking for high-resolution optical microscopy, in vivo

(2012) M. BAKALAR et al.   JOURNAL OF MICROSCOPY

Reduction of motion artifacts duringin vivotwo-photon imaging of brain through heartbeat triggered scanning

(2012) Martin Paukert et al.   JOURNAL OF PHYSIOLOGY-LONDON

Chronic in vivo imaging in the mouse spinal cord using an implanted chamber

(2012) Matthew J Farrar et al.   NATURE METHODS

High Resolution Intravital Imaging of Subcellular Structures of Mouse Abdominal Organs Using a Microstage Device

(2012) Liqin Cao et al.   PLoS One

Real-time in vivo imaging of the beating mouse heart at microscopic resolution

(2012) Sungon Lee et al.   Nature Communications

Fibrinogen-induced perivascular microglial clustering is required for the development of axonal damage in neuroinflammation

(2012) Dimitrios Davalos et al.   Nature Communications

Intravital Imaging

(2011) Mikael J. Pittet et al.   CELL

Recent advances in dynamic intravital multi-photon microscopy

(2011) Raluca A. Niesner et al.   CYTOMETRY PART A

Digital correction of motion artefacts in microscopy image sequences collected from living animals using rigid and nonrigid registration

(2011) K. S. LORENZ et al.   JOURNAL OF MICROSCOPY

A reversible form of axon damage in experimental autoimmune encephalomyelitis and multiple sclerosis

(2011) Ivana Nikić et al.   NATURE MEDICINE

Miniaturized integration of a fluorescence microscope

(2011) Kunal K Ghosh et al.   NATURE METHODS

Functional Specialization of Mouse Higher Visual Cortical Areas

(2011) Mark L. Andermann et al.   NEURON

Adaptive Movement Compensation for In Vivo Imaging of Fast Cellular Dynamics within a Moving Tissue

(2011) Sophie Laffray et al.   PLoS One

Intravital imaging of phagocyte recruitment

(2011) Klaus Kemmerich et al.   THROMBOSIS AND HAEMOSTASIS

Hyperlipidemia-Triggered Neutrophilia Promotes Early Atherosclerosis

(2010) Maik Drechsler et al.   CIRCULATION

Short Communication: Subcellular Motion Compensation for Minimally Invasive Microscopy, In Vivo

(2010) James L. Schroeder et al.   CIRCULATION RESEARCH

Nonrigid Image Registration Using Conditional Mutual Information

(2010) D. Loeckx et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

In vivo high-resolution structural imaging of large arteries in small rodents using two-photon laser scanning microscopy

(2010) Remco T. A. Megens et al.   JOURNAL OF BIOMEDICAL OPTICS

In vivoCa2+imaging of dorsal horn neuronal populations in mouse spinal cord

(2010) Helge C. Johannssen et al.   JOURNAL OF PHYSIOLOGY-LONDON

Chronic optical access through a polished and reinforced thinned skull

(2010) Patrick J Drew et al.   NATURE METHODS

Stabilized imaging of immune surveillance in the mouse lung

(2010) Mark R Looney et al.   NATURE METHODS

Broadly Tuned Response Properties of Diverse Inhibitory Neuron Subtypes in Mouse Visual Cortex

(2010) Aaron M. Kerlin et al.   NEURON

In vivo two-photon imaging reveals monocyte-dependent neutrophil extravasation during pulmonary inflammation

(2010) D. Kreisel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optical probing of neuronal ensemble activity

(2009) Benjamin F Grewe et al.   CURRENT OPINION IN NEUROBIOLOGY

Two-photon laser scanning microscopy imaging of intact spinal cord and cerebral cortex reveals requirement for CXCR6 and neuroinflammation in immune cell infiltration of cortical injury sites

(2009) Jiyun V. Kim et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window

(2009) Anthony Holtmaat et al.   Nature Protocols

Visually evoked activity in cortical cells imaged in freely moving animals

(2009) J. Sawinski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Image Stabilization for In Vivo Microscopy by High-Speed Visual Feedback Control

(2008) Sungon Lee et al.   IEEE Transactions on Robotics

Automated correction of fast motion artifacts for two-photon imaging of awake animals

(2008) David S. Greenberg et al.   JOURNAL OF NEUROSCIENCE METHODS

Stable in vivo imaging of densely populated glia, axons and blood vessels in the mouse spinal cord using two-photon microscopy

(2007) Dimitrios Davalos et al.   JOURNAL OF NEUROSCIENCE METHODS

Microscopic imaging techniques for drug discovery

(2007) Andrew Bullen   NATURE REVIEWS DRUG DISCOVERY