Visbrain: A Multi-Purpose GPU-Accelerated Open-Source Suite for Multimodal Brain Data Visualization

We present Visbrain, a Python open-source package that offers a comprehensive visualization suite for neuroimaging and electrophysiological brain data. Visbrain consists of two levels of abstraction: (1) objects which represent highly configurable neurooriented visual primitives (3D brain, sources connectivity, etc.) and (2) graphical user interfaces for higher level interactions. The object level offers flexible and modular tools to produce and automate the production of figures using an approach similar to that of Matplotlib with subplots. The second level visually connects these objects by controlling properties and interactions through graphical interfaces. The current release of Visbrain (version 0.4.2) contains 14 different objects and three responsive graphical user interfaces, built with PyQt: Signal, for the inspection of time-series and spectral properties, Brain for any type of visualization involving a 3D brain and Sleep for polysomnographic data visualization and sleep analysis. Each module has been developed in tight collaboration with end-users, i.e., primarily neuroscientists and domain experts, who bring their experience to make Visbrain as transparent as possible to the recording modalities (e.g., intracranial EEG, scalp-EEG, MEG, anatomical and functional MRI). Visbrain is developed on top of VisPy, a Python package providing high-performance 2D and 3D visualization by leveraging the computational power of the graphics card. Visbrain is available on Github and comes with a documentation, examples, and datasets (http://visbrain.org).

MR-compatible robotics to investigate human motor control

Roger Gassert

Robotic interfaces can dynamically interact with humans performing movements and can be used to study neuromuscular adaptation. Such devices can produce computer controlled dynamics during movement and measure the interaction force and movement trajectory. On the other hand, functional magnetic resonance imaging (fMRI) can provide insight into the functional organization and plasticity of the brain. Using a robotic interface in conjunction with fMRI could allow neuroscientists to investigate the brain mechanisms of manipulation and motor learning, give therapists a tool for adaptive and patient-specific rehabilitation therapies, and assist medical doctors in functional diagnostics of motor dysfunctions. However, the MR environment imposes severe safety and electromagnetic compatibility constraints on mechatronic components, and the accessible workspace around the subject is limited. In addition, interaction with human motion must be safe and gentle. This thesis investigates the MR compatibility and performances of mechatronic elements, and develops an fMRI-compatible robotic technology consisting of sensors and actuators as well as adequate safety, control and synchronization strategies. It thus becomes possible to design various robotic systems for interaction with human motion during fMRI. This novel technology is benchmarked through the realization of several MR-compatible robotic systems which are currently being used by neuroscience groups in Japan and Europe. These include a highly MR-compatible interface for wrist motion, a tactile finger stimulation device using both intrinsically compatible and electrically powered components, as well as a two-degrees-of-freedom interface to investigate the control of multi-joint arm movements. The MR compatibility of these devices is successfully tested using a protocol developed for the particularly sensitive functional MRI sequences. In a further step towards performing multi-joint arm movements during fMRI, movement-related artifacts and biomechanical constraints are examined, and movements suitable for motor control studies are identified. Preliminary experiments with the realized systems demonstrate the potential of such robotic interfaces: the brain activation patterns during mental simulation of wrist motion are different from the patterns obtained during actual movements in interaction with the interface, and activation patterns in all conditions agree with results from literature. The well-controlled conditions as well as the recorded position and force data during fMRI open up new possibilities in data analysis and may allow new insights into the brain mechanisms involved in human motor control.

EPFL2006

Large Volume Imaging of Rodent Brain Anatomy with Emphasis on Selective Plane Illumination Microscopy

Jean Pierre Ghobril

Inside the human brain there are 86 Billion neurons exchanging electrical impulses to allow reaction, homoeostasis and intelligence. Their coarse organization has been described, leaving us with a fair understanding of macrocircuitry. The microcircuitry of the brain is also being explored with patch clamp recordings. But a more integrative view on mesoscale organization of the central nervous system is still lacking. Recent developments in microscopy methods have opened new windows to address this point. It is the goal of this thesis to analyze and compare anatomical features of the brain with current routine techniques as well as explore light sheet microscopy for large scale quantitative reconstructions of rodent brains. Integration efforts of the cortical column model of the Blue Brain project into more detailed cortical circuitry sparked the search of acute slice preparations suitable for long range electrophysiology. Serial section reconstruction of the rat S1 hindlimb anterograde projections was performed with special attention to the anatomical relationship between S1 hindlimb region and VPL nucleus of thalamus. It was found that a functional electrophysiological slice preparation between S1-HL and VPL is feasible. The subsequent experimental exploration proved the intact fiber path in acute slice preparations based on the morphometric measurements of the previous serial sectioning reconstruction. Another mesoscale trait investigated was the excitatory to inhibitory ratio of the juvenile rat cortex. The measured numbers for the cellular density are higher than previously published. Cellular density for S1-HL is 84535

\pm

4400 neurons/mm

^{3}

high with an E-I ratio of 8.3. Like in other brains the cellular density is a continuously adapting function of the distance from pia and the current brain region. In the second part of this dissertation Selective Plane Illumination Microscopy(SPIM) and tissue clearing are evaluated as novel tools for whole mount rodent brain scanning, with emphasis on somata, fibers and vasculature as quantifiable brain features. Clearing methods are evaluated and a novel embedding medium for cleared tissues is presented: Thiodiethanol(TDE). Index matched brains with TDE show high degree of fluorescence conservation and transparency. Whole mount mouse and rat brains are imaged and reconstructed. The results show that whole mount microscopy is a potent tool that allows routine quantification of anatomic features on a whole brain level.

EPFL2015

Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues

Daniya Boges, Corrado Cali, Pierre Magistretti, Madhusudhanan Srinivasan

Advances in the application of electron microscopy (EM) to serial imaging are opening doors to new ways of analyzing cellular structure. New and improved algorithms and workflows for manual and semiautomated segmentation allow us to observe the spatial arrangement of the smallest cellular features with unprecedented detail in full three-dimensions. From larger samples, higher complexity models can be generated; however, they pose new challenges to data management and analysis. Here we review some currently available solutions and present our approach in detail. We use the fully immersive virtual reality (VR) environment CAVE (cave automatic virtual environment), a room in which we are able to project a cellular reconstruction and visualize in 3D, to step into a world created with Blender, a free, fully customizable 3D modeling software with NeuroMorph plug-ins for visualization and analysis of EM preparations of brain tissue. Our workflow allows for full and fast reconstructions of volumes of brain neuropil using ilastik, a software tool for semiautomated segmentation of EM stacks. With this visualization environment, we can walk into the model containing neuronal and astrocytic processes to study the spatial distribution of glycogen granules, a major energy source that is selectively stored in astrocytes. The use of CAVE was key to the observation of a nonrandom distribution of glycogen, and led us to develop tools to quantitatively analyze glycogen clustering and proximity to other subcellular features. (c) 2015 Wiley Periodicals, Inc.

Wiley-Blackwell2016