In this application, Cellvizio was used to study the neuronal degeneration and regeneration processes in live, anaesthetized, adult Thy1-YFP transgenic mice.
1) The document discusses preliminary studies using two-photon microscopy to image brain areas of zebra finches through their thin skin and hollow skull structure for non-invasive monitoring of brain activity.
2) Experiments were conducted imaging hollow fibers filled with Rhodamine B passed through fixed zebra finch skin and skull samples to evaluate spatial resolution and distortion. Reflectance confocal measurements were also taken to determine scattering properties of fresh and fixed skin and skull.
3) The goal is to determine if two-photon microscopy can provide sufficient resolution for in vivo brain imaging and metabolism monitoring of zebra finches as a model for studying vocal recognition, without requiring craniotomy as in other small animal studies.
The document discusses using cognitive technology and sleep as an example. It describes how sleep is normally divided into cycles and stages, and how polysomnography is currently used to diagnose sleep problems. However, PSG has limitations like discomfort of wires and first night effects. The document proposes using portable devices like actigraphy watches and portable PSG systems that are more comfortable and suitable for home sleep monitoring and diagnosis. It describes developing automated sleep stage classification algorithms to analyze sleep data more efficiently.
Optical coherence tomography (OCT) is a non-invasive imaging technique that examines living tissue using low coherence radiation. OCT allows for both qualitative and quantitative analysis of the retina. Qualitatively, OCT can describe retinal structures and anomalies. Quantitatively, OCT can measure retinal thickness and nerve fiber layer thickness. OCT works by capturing 128 to 768 axial scans in a single pass, with each scan containing 1024 data points over a 2mm depth. OCT has higher resolution and penetration depth than standard clinical imaging.
The document discusses neural correlates of higher level brain functions. It covers several topics:
1) Experience arises at the quantum level in ion channel proteins, with quantum properties like coherence and entanglement playing a role.
2) Construction of perception involves transitions from quantum to classical domains in the brain, mediated by ion channel proteins. Top-down processes and long-range connections in large brains are important for conscious perception.
3) Perception emerges from complex interactions between ascending and recurrent signaling in the brain, with feedback thought to be crucial for awareness. Receptive field properties evolve along synaptic distances in hierarchical cortical networks.
BPS 2010 Poster Presentation: Shotgun DNA Mapping with YeastAnthony Salvagno
This is my poster presentation from the annual Biophysical Society Meeting in San Francisco, CA. I detail the current progress made in Shotgun DNA mapping and include an aside about open notebook science and my scientific life on the internet.
This document discusses various soft computing techniques for iris recognition, specifically focusing on two neural network approaches: Competitive neural network Learning Vector Quantization (LVQ) and Adaptive Resonance Associative Map (ARAM). It provides an overview of iris recognition as a biometric method, summarizes preprocessing steps like localization, segmentation, and normalization of iris images. It also describes feature extraction and matching steps. Finally, it defines artificial neural networks and discusses how LVQ and ARAM can be used for pattern matching in iris recognition applications.
Introduction to Spiking Neural Networks: From a Computational Neuroscience pe...Jason Tsai
The document provides an introduction to spiking neural networks (SNNs) and neuromorphic computing. It discusses the characteristics and advantages of SNNs, including their spatio-temporal nature, asynchronous processing, sparsity, and energy efficiency. It also covers basic neuroscience concepts like neurons, action potentials, synaptic plasticity, and learning rules like STDP. Common SNN models and neural encoding schemes are described. Examples of SNN applications in visual processing and pattern generation are presented. Finally, neuromorphic hardware platforms like Intel's Loihi chip are introduced.
MAGNETOM C! is a compact 0.35T MRI system with a C-shaped magnet. It offers high image quality and advanced applications in a space-efficient and patient-friendly design. The system features a multi-channel RF system that allows for simultaneous placement of up to 4 coils, as well as high-performance gradients. It provides comprehensive clinical applications for neuro, orthopedic, cardiac, body, and women's health imaging. The system aims to improve workflow and patient throughput with features such as inline processing and syngo Phoenix for protocol management.
1) The document discusses preliminary studies using two-photon microscopy to image brain areas of zebra finches through their thin skin and hollow skull structure for non-invasive monitoring of brain activity.
2) Experiments were conducted imaging hollow fibers filled with Rhodamine B passed through fixed zebra finch skin and skull samples to evaluate spatial resolution and distortion. Reflectance confocal measurements were also taken to determine scattering properties of fresh and fixed skin and skull.
3) The goal is to determine if two-photon microscopy can provide sufficient resolution for in vivo brain imaging and metabolism monitoring of zebra finches as a model for studying vocal recognition, without requiring craniotomy as in other small animal studies.
The document discusses using cognitive technology and sleep as an example. It describes how sleep is normally divided into cycles and stages, and how polysomnography is currently used to diagnose sleep problems. However, PSG has limitations like discomfort of wires and first night effects. The document proposes using portable devices like actigraphy watches and portable PSG systems that are more comfortable and suitable for home sleep monitoring and diagnosis. It describes developing automated sleep stage classification algorithms to analyze sleep data more efficiently.
Optical coherence tomography (OCT) is a non-invasive imaging technique that examines living tissue using low coherence radiation. OCT allows for both qualitative and quantitative analysis of the retina. Qualitatively, OCT can describe retinal structures and anomalies. Quantitatively, OCT can measure retinal thickness and nerve fiber layer thickness. OCT works by capturing 128 to 768 axial scans in a single pass, with each scan containing 1024 data points over a 2mm depth. OCT has higher resolution and penetration depth than standard clinical imaging.
The document discusses neural correlates of higher level brain functions. It covers several topics:
1) Experience arises at the quantum level in ion channel proteins, with quantum properties like coherence and entanglement playing a role.
2) Construction of perception involves transitions from quantum to classical domains in the brain, mediated by ion channel proteins. Top-down processes and long-range connections in large brains are important for conscious perception.
3) Perception emerges from complex interactions between ascending and recurrent signaling in the brain, with feedback thought to be crucial for awareness. Receptive field properties evolve along synaptic distances in hierarchical cortical networks.
BPS 2010 Poster Presentation: Shotgun DNA Mapping with YeastAnthony Salvagno
This is my poster presentation from the annual Biophysical Society Meeting in San Francisco, CA. I detail the current progress made in Shotgun DNA mapping and include an aside about open notebook science and my scientific life on the internet.
This document discusses various soft computing techniques for iris recognition, specifically focusing on two neural network approaches: Competitive neural network Learning Vector Quantization (LVQ) and Adaptive Resonance Associative Map (ARAM). It provides an overview of iris recognition as a biometric method, summarizes preprocessing steps like localization, segmentation, and normalization of iris images. It also describes feature extraction and matching steps. Finally, it defines artificial neural networks and discusses how LVQ and ARAM can be used for pattern matching in iris recognition applications.
Introduction to Spiking Neural Networks: From a Computational Neuroscience pe...Jason Tsai
The document provides an introduction to spiking neural networks (SNNs) and neuromorphic computing. It discusses the characteristics and advantages of SNNs, including their spatio-temporal nature, asynchronous processing, sparsity, and energy efficiency. It also covers basic neuroscience concepts like neurons, action potentials, synaptic plasticity, and learning rules like STDP. Common SNN models and neural encoding schemes are described. Examples of SNN applications in visual processing and pattern generation are presented. Finally, neuromorphic hardware platforms like Intel's Loihi chip are introduced.
MAGNETOM C! is a compact 0.35T MRI system with a C-shaped magnet. It offers high image quality and advanced applications in a space-efficient and patient-friendly design. The system features a multi-channel RF system that allows for simultaneous placement of up to 4 coils, as well as high-performance gradients. It provides comprehensive clinical applications for neuro, orthopedic, cardiac, body, and women's health imaging. The system aims to improve workflow and patient throughput with features such as inline processing and syngo Phoenix for protocol management.
The document proposes new techniques called ERASE and ERASERS for more efficiently sanitizing computer media. ERASE calculates the entropy of disk blocks and overwrites those within a sensitive entropy range. ERASERS divides the area to be wiped into subpopulations, randomly samples blocks within each, and only overwrites subpopulations containing sensitive data. The techniques were implemented in a tool and showed improvements over current methods for wiping drives of increasing size.
This document provides an introduction to deep learning in medical imaging. It explains that artificial neural networks are modeled after biological neurons and use multiple hidden layers to approximate complex functions. Convolutional neural networks are commonly used for image data, applying filters over images to extract features. Modern deep learning platforms perform cross-correlation instead of convolution for efficiency. The key process for improving deep learning models is backpropagation, which calculates the gradient of the loss function to update weights and biases in a direction that reduces loss. Deep learning has applications in medical imaging modalities like MRI, ultrasound, CT, and PET.
Charting the human thalamus - basic contepts and recent developmentsDr. Jakab András
This document summarizes a study on developing a probabilistic tractography and segmentation method to chart the human thalamus. The study used diffusion tensor imaging and probabilistic tractography to visualize cortico-thalamic connections. It then developed a statistical shape model of the mean thalamus atlas incorporating these connectivity maps. The method was able to align the atlas to individual subjects' geometry with sub-millimeter accuracy, outperforming conventional alignment methods. This individualized target mapping method could help guide image-guided neurosurgery of the thalamus.
Small animal imaging often uses micro-CT to study bone changes like osteoporosis over time. However, micro-CT exposes animals to radiation with each scan. Discrete tomography is an alternative reconstruction technique that can provide accurate reconstructions from limited projection data using prior knowledge and assumptions about object homogeneity. This allows conclusions to be drawn with less radiation exposure for longitudinal small animal studies of bone changes like osteoporosis.
Optical propagation of blue LED light in brain tissue and Parylene-C used in ...Manjunath Pujar
Understanding the propagation of LED light in the brain tissue can facilitate the advanced development of LED based neuroprosthetic devices for optogenetic applications. The attenuation coefficient of blue LED light in thin tissue slices and Parylene-C films were quantified, which is 19.9 cm-1 and 1.70 cm-1, respectively. Optical simulations in TracePro show good agreement with the experiments.
As a revolutionary neuromodulation technology, optogenetics offers remote manipulation on neural activities of genetically-targeted neural cells with millisecond temporal precision through light illumination. Compared to electrical stimulation, optogenetics has unique benefits including specificity control of neural cell types as well as minimal artifacts and instrumental interferences with electrophysiological recording. Application of optogenetics in neuroscience studies has created an increasing need for the development of light sources and the instruments for light delivery. Among various light sources, micro-light-emitting diodes (μ-LEDs) are favored for its high power efficiency, low cost, and capability of complex system integration. Successful in-vivo optogenetic stimulation on neural cells with the employment of μ-LEDs has been widely reported.
Cassandra audio-video sensor fusion for aggression detectionJoão Gabriel Lima
The document presents CASSANDRA, a system for detecting aggressive human behavior using audio-video sensor fusion. At the low level, audio and video streams are independently analyzed to extract intermediate descriptors like "scream" from audio and "articulation energy" from video. At the higher level, a Dynamic Bayesian Network fuses these descriptors and contextual knowledge to produce an aggregate aggression indication. The system was validated on scenarios performed by actors at a train station to ensure realistic noise conditions.
This document provides information about an upcoming "Multimodal Imaging in Neurosciences" course, including:
1) Dates and topics for upcoming lectures, as well as details about a final test on basic imaging techniques.
2) An overview of various neuroimaging modalities like CT, MRI, PET, and their applications.
3) A brief history of the development of high-intensity focused ultrasound (HIFU) technology from the 1880s to present.
Sleep promotes the consolidation of newly formed memories. During slow-wave sleep, slow oscillations coordinate the reactivation and redistribution of hippocampus-dependent memories to neocortical sites, supporting system consolidation. Rapid eye movement sleep supports synaptic consolidation through local increases in plasticity-related gene activity and theta oscillations in the cortex. Behavioral studies show sleep enhances retention of declarative and procedural memories, especially for explicitly encoded information. Sleep leads to quantitative strengthening and qualitative changes in memory representations.
The document discusses age-related changes in visual function based on a lecture. It covers 3 main topics:
1) Optical changes like increased light absorption and scatter in the lens and other structures, reducing retinal illumination.
2) Neural changes in the retina like loss of rods, cones and optic nerve fibers. These neural changes may underlie declines in visual functions.
3) Specific age-related changes in visual functions including reduced acuity, contrast sensitivity, dark adaptation, color vision and oculomotor abilities. Both optical and neural factors contribute to these declines.
Image Processing Technique for Brain Abnormality DetectionCSCJournals
Medical imaging is expensive and very much sophisticated because of proprietary software and expert personalities. This paper introduces an inexpensive, user friendly general-purpose image processing tool and visualization program specifically designed in MATLAB to detect much of the brain disorders as early as possible. The application provides clinical and quantitative analysis of medical images. Minute structural difference of brain gradually results in major disorders such as schizophrenia, Epilepsy, inherited speech and language disorder, Alzheimer's dementia etc. Here the main focusing is given to diagnose the disease related to the brain and its psychic nature (Alzheimer’s disease).
A maskless exposure device for rapid photolithographic prototyping of sensor ...Dhanesh Rajan
A very cost effective maskless exposure device (MED) for the fast lithographic prototyping of various layouts is presented. The device is assembled using a digital light processing projector (DLP), an optical microscope, alignment stages and a web camera. Layouts created on a computer screen can be easily transferred to substrate surfaces without using expensive photomasks and the process can be repeated by introducing new drawings on the screen. Components are tuned for a constant area of exposure and a resolution of around 20 μm is possible at the moment without using any reduction lenses. The MED has been used in patterning the surfaces of silicon, glass, metal etc. successfully. The device can be assembled using commercially available components at a very minimum cost and can be effectively used in fast prototyping applications like in MEMS, microfluidics, patterning of sensor and electrode structures.
This document discusses how micro and nanotechnologies can contribute to progress in neuroscience. It describes how technologies like MOS transistors and nanoionics/nanoelectronics can help study the structure and function of synapses at the nanoscale level. Potential applications include using these technologies to better understand basic neuroscience, as well as in clinical areas like neuronal regeneration, neuroprotection, neuromodulation, and high resolution imaging. The document advocates for an interdisciplinary approach involving neurobiologists, neurologists, engineers, and materials scientists to identify potential applications and focus technology development efforts in order to maximize the impact of these technologies and further progress in understanding the brain.
Computer vision aims to make sense of the vast amounts of visual data on the internet. It has applications for autonomous vehicles to interpret images of the road. The human visual system has over 100 billion neurons and 1000 trillion connections that allow us to perceive the world. Computer vision systems draw inspiration from the human visual cortex, with convolutional neural networks that mimic the visual hierarchy in the brain. While systems have improved at tasks like image classification, computers still lack the human ability to understand context and assign meaning based on surroundings.
This covers a end-to-end coverage of neural networks,CNN internals , Tensorflow and Keras basic , intution on object detection and face recognition and AI on Android x86.
Blindness is a serious condition that is feared by many. Researchers are working on developing artificial vision technologies to help restore sight for the blind. One such technology is a bionic eye, which uses a camera and implant to stimulate the retina and optic nerve to generate images in the brain. The retina plays a key role in vision, containing rods, cones and ganglion cells that transmit light signals to the brain. Retinal diseases can lead to blindness by damaging these cells. Researchers are working to bypass damaged areas and provide artificial stimulation to restore some level of sight.
Week 1. Basics of multimodal imaging and image processing. Functional magneti...Dr. Jakab András
This document discusses multimodal neuroimaging. It provides an introduction to combining multiple imaging modalities such as CT, MRI, PET, and EEG to gain complementary information. Key benefits of multimodal imaging include anatomical alignment of images and fusion of structural and functional data. Examples of hybrid imaging devices that facilitate multimodal approaches are PET-CT and PET-MRI scanners. The document also gives an overview of functional MRI techniques for mapping brain activity and networks involved in sensory, motor, cognitive and resting state functions.
The document discusses various methods for providing artificial vision to blind individuals, including digital artificial vision using a miniature camera, microchip, and electrode array implanted in the occipital lobe of the brain. The camera feeds images to a microcomputer for edge detection processing before electrical signals are sent to each electrode to simulate vision. The electrodes are implanted by piercing a platinum foil ground plate inserted into the skull. This allows blind individuals to perceive visual stimuli through artificial stimulation of the visual cortex.
White Paper: In vivo Fiberoptic Fluorescence Microscopy in freely behaving miceFUJIFILM VisualSonics Inc.
Fiberoptic fluorescence microscopy (FFM) employs optical fibers as small as 300 micrometers in diameter and offers the ability to image cellular and subcellular processes in deep brain structures including the Ventral Tegmental Area (VTA) and the substantia nigra (Sn).
1) ShearWave Elastography provides quantitative elasticity maps in real-time by measuring shear wave propagation speed induced by acoustic radiation force from an ultrasound beam. Stiffer tissues are coded in red and softer tissues in blue.
2) Shear waves are generated using SonicTouch technology which focuses ultrasound beams at different depths to coherently sum shear waves in a Mach cone shape, amplifying their amplitude.
3) UltraFast imaging is needed to capture shear wave propagation, with frame rates of thousands per second, achieved using plane waves to insonify the full imaging plane at once.
The document proposes new techniques called ERASE and ERASERS for more efficiently sanitizing computer media. ERASE calculates the entropy of disk blocks and overwrites those within a sensitive entropy range. ERASERS divides the area to be wiped into subpopulations, randomly samples blocks within each, and only overwrites subpopulations containing sensitive data. The techniques were implemented in a tool and showed improvements over current methods for wiping drives of increasing size.
This document provides an introduction to deep learning in medical imaging. It explains that artificial neural networks are modeled after biological neurons and use multiple hidden layers to approximate complex functions. Convolutional neural networks are commonly used for image data, applying filters over images to extract features. Modern deep learning platforms perform cross-correlation instead of convolution for efficiency. The key process for improving deep learning models is backpropagation, which calculates the gradient of the loss function to update weights and biases in a direction that reduces loss. Deep learning has applications in medical imaging modalities like MRI, ultrasound, CT, and PET.
Charting the human thalamus - basic contepts and recent developmentsDr. Jakab András
This document summarizes a study on developing a probabilistic tractography and segmentation method to chart the human thalamus. The study used diffusion tensor imaging and probabilistic tractography to visualize cortico-thalamic connections. It then developed a statistical shape model of the mean thalamus atlas incorporating these connectivity maps. The method was able to align the atlas to individual subjects' geometry with sub-millimeter accuracy, outperforming conventional alignment methods. This individualized target mapping method could help guide image-guided neurosurgery of the thalamus.
Small animal imaging often uses micro-CT to study bone changes like osteoporosis over time. However, micro-CT exposes animals to radiation with each scan. Discrete tomography is an alternative reconstruction technique that can provide accurate reconstructions from limited projection data using prior knowledge and assumptions about object homogeneity. This allows conclusions to be drawn with less radiation exposure for longitudinal small animal studies of bone changes like osteoporosis.
Optical propagation of blue LED light in brain tissue and Parylene-C used in ...Manjunath Pujar
Understanding the propagation of LED light in the brain tissue can facilitate the advanced development of LED based neuroprosthetic devices for optogenetic applications. The attenuation coefficient of blue LED light in thin tissue slices and Parylene-C films were quantified, which is 19.9 cm-1 and 1.70 cm-1, respectively. Optical simulations in TracePro show good agreement with the experiments.
As a revolutionary neuromodulation technology, optogenetics offers remote manipulation on neural activities of genetically-targeted neural cells with millisecond temporal precision through light illumination. Compared to electrical stimulation, optogenetics has unique benefits including specificity control of neural cell types as well as minimal artifacts and instrumental interferences with electrophysiological recording. Application of optogenetics in neuroscience studies has created an increasing need for the development of light sources and the instruments for light delivery. Among various light sources, micro-light-emitting diodes (μ-LEDs) are favored for its high power efficiency, low cost, and capability of complex system integration. Successful in-vivo optogenetic stimulation on neural cells with the employment of μ-LEDs has been widely reported.
Cassandra audio-video sensor fusion for aggression detectionJoão Gabriel Lima
The document presents CASSANDRA, a system for detecting aggressive human behavior using audio-video sensor fusion. At the low level, audio and video streams are independently analyzed to extract intermediate descriptors like "scream" from audio and "articulation energy" from video. At the higher level, a Dynamic Bayesian Network fuses these descriptors and contextual knowledge to produce an aggregate aggression indication. The system was validated on scenarios performed by actors at a train station to ensure realistic noise conditions.
This document provides information about an upcoming "Multimodal Imaging in Neurosciences" course, including:
1) Dates and topics for upcoming lectures, as well as details about a final test on basic imaging techniques.
2) An overview of various neuroimaging modalities like CT, MRI, PET, and their applications.
3) A brief history of the development of high-intensity focused ultrasound (HIFU) technology from the 1880s to present.
Sleep promotes the consolidation of newly formed memories. During slow-wave sleep, slow oscillations coordinate the reactivation and redistribution of hippocampus-dependent memories to neocortical sites, supporting system consolidation. Rapid eye movement sleep supports synaptic consolidation through local increases in plasticity-related gene activity and theta oscillations in the cortex. Behavioral studies show sleep enhances retention of declarative and procedural memories, especially for explicitly encoded information. Sleep leads to quantitative strengthening and qualitative changes in memory representations.
The document discusses age-related changes in visual function based on a lecture. It covers 3 main topics:
1) Optical changes like increased light absorption and scatter in the lens and other structures, reducing retinal illumination.
2) Neural changes in the retina like loss of rods, cones and optic nerve fibers. These neural changes may underlie declines in visual functions.
3) Specific age-related changes in visual functions including reduced acuity, contrast sensitivity, dark adaptation, color vision and oculomotor abilities. Both optical and neural factors contribute to these declines.
Image Processing Technique for Brain Abnormality DetectionCSCJournals
Medical imaging is expensive and very much sophisticated because of proprietary software and expert personalities. This paper introduces an inexpensive, user friendly general-purpose image processing tool and visualization program specifically designed in MATLAB to detect much of the brain disorders as early as possible. The application provides clinical and quantitative analysis of medical images. Minute structural difference of brain gradually results in major disorders such as schizophrenia, Epilepsy, inherited speech and language disorder, Alzheimer's dementia etc. Here the main focusing is given to diagnose the disease related to the brain and its psychic nature (Alzheimer’s disease).
A maskless exposure device for rapid photolithographic prototyping of sensor ...Dhanesh Rajan
A very cost effective maskless exposure device (MED) for the fast lithographic prototyping of various layouts is presented. The device is assembled using a digital light processing projector (DLP), an optical microscope, alignment stages and a web camera. Layouts created on a computer screen can be easily transferred to substrate surfaces without using expensive photomasks and the process can be repeated by introducing new drawings on the screen. Components are tuned for a constant area of exposure and a resolution of around 20 μm is possible at the moment without using any reduction lenses. The MED has been used in patterning the surfaces of silicon, glass, metal etc. successfully. The device can be assembled using commercially available components at a very minimum cost and can be effectively used in fast prototyping applications like in MEMS, microfluidics, patterning of sensor and electrode structures.
This document discusses how micro and nanotechnologies can contribute to progress in neuroscience. It describes how technologies like MOS transistors and nanoionics/nanoelectronics can help study the structure and function of synapses at the nanoscale level. Potential applications include using these technologies to better understand basic neuroscience, as well as in clinical areas like neuronal regeneration, neuroprotection, neuromodulation, and high resolution imaging. The document advocates for an interdisciplinary approach involving neurobiologists, neurologists, engineers, and materials scientists to identify potential applications and focus technology development efforts in order to maximize the impact of these technologies and further progress in understanding the brain.
Computer vision aims to make sense of the vast amounts of visual data on the internet. It has applications for autonomous vehicles to interpret images of the road. The human visual system has over 100 billion neurons and 1000 trillion connections that allow us to perceive the world. Computer vision systems draw inspiration from the human visual cortex, with convolutional neural networks that mimic the visual hierarchy in the brain. While systems have improved at tasks like image classification, computers still lack the human ability to understand context and assign meaning based on surroundings.
This covers a end-to-end coverage of neural networks,CNN internals , Tensorflow and Keras basic , intution on object detection and face recognition and AI on Android x86.
Blindness is a serious condition that is feared by many. Researchers are working on developing artificial vision technologies to help restore sight for the blind. One such technology is a bionic eye, which uses a camera and implant to stimulate the retina and optic nerve to generate images in the brain. The retina plays a key role in vision, containing rods, cones and ganglion cells that transmit light signals to the brain. Retinal diseases can lead to blindness by damaging these cells. Researchers are working to bypass damaged areas and provide artificial stimulation to restore some level of sight.
Week 1. Basics of multimodal imaging and image processing. Functional magneti...Dr. Jakab András
This document discusses multimodal neuroimaging. It provides an introduction to combining multiple imaging modalities such as CT, MRI, PET, and EEG to gain complementary information. Key benefits of multimodal imaging include anatomical alignment of images and fusion of structural and functional data. Examples of hybrid imaging devices that facilitate multimodal approaches are PET-CT and PET-MRI scanners. The document also gives an overview of functional MRI techniques for mapping brain activity and networks involved in sensory, motor, cognitive and resting state functions.
The document discusses various methods for providing artificial vision to blind individuals, including digital artificial vision using a miniature camera, microchip, and electrode array implanted in the occipital lobe of the brain. The camera feeds images to a microcomputer for edge detection processing before electrical signals are sent to each electrode to simulate vision. The electrodes are implanted by piercing a platinum foil ground plate inserted into the skull. This allows blind individuals to perceive visual stimuli through artificial stimulation of the visual cortex.
White Paper: In vivo Fiberoptic Fluorescence Microscopy in freely behaving miceFUJIFILM VisualSonics Inc.
Fiberoptic fluorescence microscopy (FFM) employs optical fibers as small as 300 micrometers in diameter and offers the ability to image cellular and subcellular processes in deep brain structures including the Ventral Tegmental Area (VTA) and the substantia nigra (Sn).
1) ShearWave Elastography provides quantitative elasticity maps in real-time by measuring shear wave propagation speed induced by acoustic radiation force from an ultrasound beam. Stiffer tissues are coded in red and softer tissues in blue.
2) Shear waves are generated using SonicTouch technology which focuses ultrasound beams at different depths to coherently sum shear waves in a Mach cone shape, amplifying their amplitude.
3) UltraFast imaging is needed to capture shear wave propagation, with frame rates of thousands per second, achieved using plane waves to insonify the full imaging plane at once.
The document discusses image recognition using convolutional neural networks (CNNs). It explains that CNNs consist of multiple layers of small neuron collections that look at small portions of an input image called receptive fields. The results are tiled to overlap and represent the original image better. CNNs learn filters through training rather than relying on hand-engineered features. Convolution involves calculating the overlap between functions as one is translated, and is used in CNNs to identify patterns across translated versions of inputs like images. Pointwise nonlinearities are applied between CNN layers to introduce nonlinearity.
This document discusses various techniques for studying the brain, including:
- Diffusion Spectrum Imaging (DSI) allows mapping of axonal trajectories but not individual neurons due to MRI resolution limitations.
- Two-photon microscopy can image live mouse brains up to 1mm depth. Confocal laser scanning microscopy provides high-resolution images of brain structures in vitro.
- Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) provide the highest magnifications up to 1 million times but require thin samples and only work in vitro.
This document discusses hyperspectral microscopy, which combines microscopy and spectral imaging to produce data-rich views of biological structures. Hyperspectral microscopy grew from combining microspectrophotometry and spectral remote sensing. Recent advances integrated hardware and software to enable commercial hyperspectral microscopy systems. The document describes a hyperspectral microscope developed to study nanoparticles, which provides brighter dark-field illumination than conventional methods and enables spectral analysis of particle clusters. Applications demonstrated include identifying titanium dioxide nanoparticles and analyzing anthrax spores.
This document provides an overview of confocal microscopy. It discusses the history, pioneering by Minsky in 1955, instrumental design, working principles and mechanisms. The key principles are point-by-point illumination and rejection of out-of-focus light using pinholes. Applications include analysis of fluorescently labeled thick specimens without sectioning. Advantages are better resolution and ability to generate 3D data. Limitations include inherent resolution limits, dependence on fluorophores, and photobleaching effects.
Mapping Inhibitory Neuronal Ircuits By Laser Scanning Photostimula TionTaruna Ikrar
1) The document describes a technique called laser scanning photostimulation (LSPS) combined with whole-cell patch clamp recording to map local inhibitory neuronal circuits.
2) LSPS uses laser pulses to selectively activate neurons via glutamate uncaging, allowing mapping of excitatory and inhibitory synaptic inputs onto recorded neurons from many stimulation sites.
3) An example is provided showing excitatory synaptic input maps for a fast-spiking inhibitory interneuron in mouse somatosensory cortex, revealing strong input from layer 4 and deeper layers.
Stevenson Eye Tracking With The Adaptive Optics Scanning Laser OphthalmoscopeKalle
Recent advances in high magnification retinal imaging have allowed for visualization of individual retinal photoreceptors, but these systems also suffer from distortions due to fixational eye motion. Algorithms developed to remove these distortions have the added benefit of providing arc second level resolution of the eye movements that produce them. The system also allows for visualization of targets on the retina, allowing for absolute retinal position measures to the level of individual cones. This paper will describe the process used to remove the eye movement artifacts and present analysis of their spectral characteristics. We find a roughly 1/f amplitude spectrum similar to that reported by Findlay (1971) with no evidence for a distinct
tremor component.
The Nobel Prize in Chemistry 2014 was awarded to Eric Betzig, Stefan W. Hell and William E. Moerner for developing super resolved fluorescence microscopy. Super resolution microscopy uses fluorescence imaging techniques to achieve resolutions below the classical diffraction limit and allows study of subcellular structures at the nanoscale. It generates high resolution images from lower resolution images. Super resolution microscopy has advantages like observation at depth within samples, enhanced resolving power below 200nm, and ability to obtain 3D time-lapse images. However, it still requires expertise and time for complex experimental design, sample preparation, system calibration and data analysis.
Nanotechnology provides tools for understanding and treating disease at the nanoscale. Nanomaterials can interact specifically with biological components like proteins and DNA, allowing them to induce or stop metabolic reactions. These nanomaterials are also used in miniaturized diagnostic devices like biosensors and lab-on-a-chip technologies to provide fast, sensitive analysis from small samples without a laboratory. Nanosized drug delivery systems aim to target drugs solely to diseases, quickly and accurately, by entrapping or encapsulating drugs within polymer scaffolds or reservoirs at the nanoscale to reduce side effects.
Areas of cortex that receive input from more than one sensory system are called association cortex. The chemical senses refer to our ability to process the environmental stimuli of smell and taste. The olfactory receptor cells are located in the upper part of the nose, embedded in a layer of mucus-covered tissue called the olfactory mucosa.
Neuro-technology aims to restore or improve human nervous system function through electronics. Neuromotor prostheses (NMPs) extract signals from the nervous system to control devices. The goal of NMPs is to convey motor control intent from the central nervous system to drive multi-degree of freedom prosthetic devices for amputees or paralyzed patients. Key challenges are developing neural interfaces that last a lifetime and providing dexterous, natural control of prosthetics. NMP systems involve neural implants to record brain signals, decoding software to translate signals into motor commands, and output devices like prosthetics. Technological advances now allow basic NMP control but further progress is still needed.
This document describes a new ultrafast Diffuse Optical Tomography (DOT) technique developed for real-time in vivo brain imaging of songbirds. The technique uses an amplified ultrafast laser and single-shot streak camera to measure the time of flight of photons through brain tissue. This allows for a 3D reconstruction of brain activity from space and time sampling of the reflectance signal. Preliminary results show the brain tissue response to hypercapnia stimulations can be detected.
Confocal microscopy allows high-resolution imaging of the cornea. It works by only focusing on a single point and eliminating out-of-focus light to view corneal structures with 1-2 μm lateral and 5-10 μm axial resolution. This allows visualization of the epithelium, subepithelial nerves, stroma, and endothelium. Confocal microscopy is useful for evaluating corneal diseases like keratoconus and dystrophies by identifying morphological changes to these layers.
Microdialysis is an integral part of preclinical research to determine extracellular fluid and blood concentrations of metabolites, hormones, drugs, etc, and is often used in quantifying the biochemistry of brain and peripheral tissues. However, it is a molecular-only technique and other imaging modalities are needed to provide the researcher with functional and anatomical information of the animal in vivo.
The document summarizes the development and validation of a hyperspectral imaging microscopy system called Xanoscope for pathology applications. Key points:
1) Xanoscope allows for fast, automated acquisition of hyperspectral images over contiguous wavelength bands with high spatial resolution, reducing scan times significantly compared to previous methods.
2) Validation experiments showed Xanoscope produces quantitative measurements and improves signal-to-noise ratio through optimized camera settings and image accumulation.
3) Xanoscope was used to scan 10 multiplexed fluorophores in cell lines, and linear unmixing was able to measure the individual contribution of each fluorophore at pixel-level for advanced pathological analysis.
Confocal microscopy was invented by Marvin Minsky in 1957 and aims to improve resolution over traditional microscopy. It uses point illumination and a pinhole to exclude out-of-focus light and produce thin optical sections and high-contrast images. The key components are a laser light source, dichromatic mirror, pinholes, and photodetector. Confocal microscopy finds applications in cell biology and materials science by allowing optical sectioning and 3D reconstruction. It provides advantages like non-invasiveness, live cell imaging, and depth analysis, but has disadvantages such as photobleaching and loss of intensity.
Human recognition system based on retina vascular network characteristicscbnaikodi
This document proposes a human recognition system based on retina vascular network characteristics. The system uses fundus images of a person's retina as input. It performs pre-processing such as histogram equalization and edge detection using techniques like Sobel and Prewitt filters. It then compares the processed retina image to images stored in a database. If a matching image is found, the person is authorized, otherwise they are unauthorized. The system can accurately authenticate individuals and has applications in security environments like banking, military, and government that require high security.
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1. Application Note
Neuroscience: Peripheral Nerve Imaging
Introduction Each microprobe comprises tens The suitability of the Cellvizio for
of thousands of individual fiber high resolution imaging of live
This application note describes: optics encased within a single structures will provide scientists
probe. ProFlex Microprobes are the first real opportunity to perform
• The establishment of a mouse available in a range of diameters unique biomedical research studies
model of nerve degeneration and from 4.2 mm down to 300 µm. such as:
regeneration induced by a crush The small size and flexibility of the
injury to the saphenous nerve. microprobes enable direct access • The measurement of
to a region of interest within a
• The use of Cellvizio’s novel regenerative nerve outgrowth
living animal either externally,
imaging technology of Fibered • The evaluation of fiber density in
endoscopically or via a minimally
Confocal Fluorescence tissue reinnervation
invasive procedure.
Microscopy, which enables
a minimally invasive and • The analysis of the formation and
Coupled to the Laser Scanning Unit
longitudinal monitoring of the number of nerve endings to
(LSU) and ImageCell, the image
the axonal degeneration and evaluate the functional recovery
processing software, the system
regeneration processes. of neurotransmission
renders realtime dynamic image
sequences with a lateral resolution
Materials and Methods
as fine as 1.4 µm and at 12 frames
In this application, Cellvizio per second (with capabilities up to
was used to study the neuronal 200 frames per second).
degeneration and regeneration
In Vivo Imaging of Peripheral CELLULAR BODIES
processes in live, anaesthetized,
Nervous System
adult Thy1-YFP transgenic mice.
The Cellvizio has already proven
A small 2 mm incision was first its suitability for live imaging of
made in the skin, through which a the peripheral nervous system.
handheld microprobe of Using transgenic mice strains with
650 µm diameter was directly YFP-positive nervous system, the
inserted. The saphenous nerve Cellvizio images cellular bodies
was then imaged through the (Figure A), axon bundles (Figure
perineurium, allowing repeated B) and single axons (Figure C),
measurements to be made which could be followed over long
without nerve damage. This distances with the ProFlex. Figure A - Cellular bodies in the dorsal
novel technology marked to in root ganglia
vitro imaging with a traditional In addition, images of small
fluorescence microscope. nervous structures such as
dendritic endings (Figure D), AXON BUNDLE
The Cellvizio® LAB is a complete axonal endings (Figure E) and
imaging system based on a fibered neuromuscular junctions (Figure
technology for fluorescence F) are readily accessible with ease
confocal imaging of the living and minimal invasiveness. Steady
animal. It acquires high resolution image sequences can be acquired
image sequences, displays using the handheld ProFlex or
them in real-time, enables live by securing the ProFlex into an
measurements and stores the appropriate holding device.
image sequences.
The images shown represent single
The ProFlex™ Microprobe is a frames extracted from image
highly advanced optical imaging sequences obtained by following Figure B - Sciatic nerve imaged at
tool incorporating proprietary fiber the structures over long distances 5 µm lateral resolution, permitting
optic objective lens technology. and time. visualization of single axons
Application Note: Peripheral Nerve Imaging 1
2. ISOLATED FIBER Crush Injury of the Saphenous An epifluorescence microscope was
Nerve used, with a 10x/0.30 objective.
A mouse model of nerve Images acquired using both
regeneration induced by crush techniques are shown. The image
injury of the saphenous nerve, of the explanted and fixed nerve,
which includes both motor and marked by a schematic microscope
sensory fibers, was used. (Figure 2), was obtained using
The saphenous nerve, located at a tabletop epifluorescence
the anterior face of the posterior microscope. The explanted nerve
leg (Figure 1), was selected for its was fixed uncut in formaldehyde
superficial location providing easy for one hour and then observed.
Figure C - Single nerve fiber of the
cutaneous sensory network, which can access through a two millimeter
incision of the skin. These images were compared to
be followed over several millimeters
images of the saphenous nerve
DENDRITIC ENDINGS The crush induces the degeneration acquired in vivo and in situ using a
of the distal nerve fragments prior Cellvizio.
to their disappearing following
Wallerian degeneration. Figure 3 shows the axon bundle
This process is slow and takes before (top) and after (bottom) the
several days. In the meantime, crush. It is important to note that
nerve fibers begin to regenerate the nerve is being viewed through
from the injury site along the initial the perineurium, without damaging
path towards the distal stump. the nerve tissue, which made
it possible to monitor the axon
The goal was to provide a direct regeneration process repetitively
and rapid monitoring of the axon over several days.
Figure D - Terminals of a sensory fiber degeneration and regeneration
imaged under skin processes, in a live animal without Experimental Setup
tissue sampling.
AXONAL ENDINGS Adult male Thy1-YFP transgenic
Images and measurements mice (ref.: B6.Cg-Tg (Thy1-
obtained with the Cellvizio YFP)16Jrs/J, Jackson Laboratories;
were bench-marked against Feng et al., 2000) were
those obtained using standard anesthetized with intra-peritoneal
fluorescence microscopy. injections of ketamine.
Adult THY1-YFP Mouse
Figure E - Motor nerve terminals of a
b
neuromuscular junction
NEUROMUSCULAR JUNCTIONS a
Figure 1 - (a) Saphenous nerves on the underside of the posterior legs,
chosen for their superficial location (b) ProFlex™ probe allowing easy access
Figure F - Neuromuscular junctions, through a minimally-invasive incision of the skin
showing both nerve and muscle fibers.
Visualization of the muscle fiber made
possible with Syto 13
Application Note: Peripheral Nerve Imaging 2
3. In vitro explanted and fixed nerve Post-Crush Outgrowth Measurement
The tiled image of a fixed explanted nerve viewed under a standard
fluorescence microscope, four days after the crush (top of Figure 4), shows
the regeneration of axons from the crush site, the front of progression
and the remaining degenerative fragments. The crush site presents no
staining, probably due to the loss of the fluorescent agent (YFP is soluble)
during the manipulation for tissue sampling. The fiber ends of the front of
progression are visible in the debris from Wallerian degeneration (see the
high magnification images on Figure 4).
Figure 2 - Explanted, fixed and
uncut saphenous nerve acquired with In the corresponding images acquired using the Cellvizio, we can clearly
an epifluorescence microscope identify the zone of degeneration, the zone of regeneration (bottom left of
Figure 4) and the front of progression (bottom right of Figure 4) despite
the lower contrast caused by imaging through the perineurium. In dynamic
In vivo and in situ dynamic acquisition sequences, the front of progression is even more clearly visible.
It is therefore possible to visualize nerve regeneration and to measure the
length of outgrowth using a graduated wire applied along the nerve, both
without tissue biopsy.
Crush Regenerative Axons Front of Progression Degenerative Fragments
1 mm
Epifluorescence
Microscope
Figure 3 - Saphenous nerve acquired
in vivo and in situ with the Cellvizio
both, before (top) and after (bottom)
the crush. The crush induces a
rapid loss of fluorescence at the
sight of injury, probably due to the Cellvizio® LAB
solubilization of the YFP-protein.
Figure 4: Four Days After Crush - Top: Tiled image of the saphenous nerve from the
crush site to the degenerative fragments, as well as high magnification images of
the regenerative segments and the front of progression, all from an epifluorescence
Each 2 posterior leg was shaved microscope. Bottom: Cellvizio Images of the regenerative segments and the front of
over a 0.5 cm area, in order to progression with ends of regenerative nerves clearly visible. The bottom right image
visualize the saphenous vein, which was constructed by tiling images from a dynamic sequence acquired with Cellvizio.
runs along the saphenous nerve.
Fibered Confocal Fluorescence Microscopy
A 2 mm cut was made above the
vein. The model consists in the Figure 5 - Length
production of a crush injury to the of outgrowth
saphenous nerve with a ligature measured, on a
maintained for two minutes. total of 30 mice,
after a crush of
The degeneration and regeneration the saphenous
processes can then be monitored nerve, both with
over multiple days by opening and an epifluorescence
microscope (yellow)
suturing the small cut as needed.
and the Cellvizio
(blue).
Application Note: Peripheral Nerve Imaging 3
4. Axonal outgrowth was measured Crush Degenerative Fragments
in three groups of ten mice using
both a standard fluorescence
microscope and a Cellvizio. The
graph in Figure 5 displays the
results.
1 mm
• Both methodologies show that
the length of the outgrowth
Epifluorescence
increases from Day 3 to Day 5 Microscope
after the crush, as reported by
Pan et al; 2003
• In both cases, this approach has
a high reproducibility, as seen
from the low standard deviations
• The measurements of the axonal Cellvizio®
outgrowth using a Cellvizio LAB
reveals a very high correlation
Figure 6 - Four Days After Crush with vincristine administration - Top: Tiled image
with those obtained from a and high resolution images of the saphenous nerve obtained with epifluorescence
microscope microscope, depicting the crush site and no regenerative segments within the debris
of Wallerian degeneration. Bottom: Visualization of same sections using the Cellvizio
• However, the actual lengths of
the outgrowth were 30% greater, To quantify the effects of vincristine The measurements taken from
on average, when measured on nerve regeneration, four mice images acquired by the Cellvizio
using a Cellvizio. The reduced were administered a one-time dose show that the vincristine
length of the sampled nerve of vincristine on Day 1 after the transiently inhibits the regeneration
observed under a standard crush and another four mice were of axons from Day 1 to Day 6
fluorescence microscope is administered an injection of saline after the crush, as reported in
probably a result of the retraction on Day 1 after the crush. the literature (Ruigt et al., 1995;
of the nerve segment due to the Shiraishi et al., 1985; Nakamura et
section and the immersion in a The Cellvizio was used to analyze, al., 2001; Paydarfar JA and Paniello
fixative solution measure and compare the RC, 2001). Regrowth then occurs
outgrowth length over fifteen days to reach maximal length by Day
Effect of Vincristine on Nerve (Figure 7). 15.
Regeneration After a Crush
The next step in the development Fibered Confocal Fluorescence Microscopy
of this model was to test the
administration of a neurotoxic
drug, such as vincristine.
Vincristine, a chemotherapeutic
molecule, was administered at
0.5 mg/kg in a one-shot intra-
peritoneal injection on Day 1 after
the crush. High doses of vincristine
are known to induce peripheral
neuropathy and transiently block
nerve regeneration.
As depicted in both imaging
modalities (Figure 6) at Day 4
after the crush, vincristine blocks
the regeneration process. Both
the Cellvizio and the standard
fluorescence microscope show Figure 7 - Cellvizio measurement of the effect of vincristine on nerve regeneration
nerve debris of degenerating axons after crush. Pink: Test group of four mice receiving an intra-peritoneal injection of
and no regrowing fibers. 0.5 mg/kg of vincristine at Day 1 after the crush. Orange: Control group of four
mice receiving only saline.
Application Note: Peripheral Nerve Imaging 4
5. Tabletop Fluorescence Microscopy Fibered Confocal Fluorescence Microscopy
• Sacrificed animal • Live, anesthetized animal
• Explanted and fixed nerve • In vivo and in situ imaging
• Repeated measurement on the same
• One mouse per measurement mouse
• 50 minutes per measurement • 5 minutes per measurement
As demonstrated the images acquired using a Cellvizio provide a reliable approach to the imaging of the
peripheral nervous system as validated by comparison with studies using standard fluorescence microscopy.
Repetitive Measurements
The minimally invasive access in a living animal allows repetitive measurements in time, as opposed to a single
measurement session from one sacrificed mouse in regular microscopy, and a follow-up analysis of regeneration
on the same animal.
Time of Measurements
It takes about 50 minutes to measure one regenerating nerve with a microscope on account of tissue sampling,
fixation, mounting, and microscope and camera preparation. In comparison, the Cellvizio can reduce the time per
measurement to 5 minutes from incision to post-measurement suture.
In conclusion, imaging peripheral nerves with the Cellvizio provides reliable results which are in accordance to
published literature and have been benchmarked against standard fluorescence microscopy. The instrument
is easy to use. As access is only minimally invasive and there is no tissue sampling, the Cellvizio provides a
better and more time-efficient alternative for longitudinal monitoring of axonal degeneration and regeneration
processes, measurement of length of outgrowth and monitoring the effect of neurotoxic, neurotrophic and
protective molecules.
Summary
Viewing the neuronal It enables longitudinal monitoring of the
degeneration and degeneration and regeneration processes,
regeneration in situ, in a as well as the measurement of the length
living animal, has many of the nerve outgrowth. Furthermore, it
significant advantages as significantly reduces the time necessary
compared to traditional for measurement by a factor of ten. The
fluorescence microscopy. Cellvizio® LAB is the only system available
that enables in vivo and in situ molecular
imaging of peripheral nerves down to the
resloution of single axons.
Application Note: Peripheral Nerve Imaging 5
6. Credits and References
This work was published in: Pierre Vincent, Uwe Maskos,
Igor Charvet, Laurence Bourgeais, Luc Stoppini, Nathalie
Leresche, Jean-Pierre Changeux, Régis Lambert, Paolo
Meda, Danièle Paupardin-Tritsch. “Live imaging of
neural structure and function by fibered fluorescence
microscopy.” (2006) EMBO Reports 7, 11, 1154–1161”
1. Y.Albert Pan, Thomas Misgeld, Jeff W. Lichtman,
and Joshua R. Sanes (2003) Effects of Neurotoxic
and Neuroprotective Agents on Peripheral Nerve
Regeneration Assayed by Time-Lapse Imaging In
Vivo. The Journal of Neuroscience 23(36):11479-
11488
2. Feng G, Mellor RH, Bernstein M, Keller-Peck C,
Nguyen QT, Wallace M, Nerbonne JM, Lichtman
JW, Sanes JR. (2000) Imaging neuronal subsets in
transgenic mice expressing multiple spectral variants
of GFP. Neuron. 28(1):41-51
3. Ruigt GS, den Brok MH. (1995) Retardation of rat
sciatic nerve regeneration after local application
of minute doses of vincristine. Cancer Chemother.
Pharmacol. 36(6):530-5
4. Shiraishi S, Le Quesne PM, Gajree T. (1985) The
effect of vincristine on nerve regeneration in the
rat. An electro¬physiological study. J Neurol. Sci.
71(1):9-17
5. Nakamura Y, Shimizu H, Nishijima C, Ueno M,
Arakawa Y. (2001) Delayed functional recovery by
vincristine after sciatic nerve crush injury: a mouse
model of vincristine neurotoxicity. Neurosci. Lett.
304: 5-8
6. Paydarfar JA, Paniello RC (2001) Functional study
of four neurotoxins as inhibitors of post-traumatic
nerve regeneration. Laryngoscope 111: 844-850
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Application Note: Peripheral Nerve Imaging 6