High-Throughput Method of Whole-Brain Sectioning, Using the Tape-Transfer Technique

Cryostat sectioning is a popular but labor-intensive method for preparing histological brain sections. We have developed a modification of the commercially available CryoJane tape collection method that significantly improves the ease of collection and the final quality of the tissue sections. The key modification involves an array of UVLEDs to achieve uniform polymerization of the glass slide and robust adhesion between the section and slide. This report presents system components and detailed procedural steps, and provides examples of end results; that is, 20mum mouse brain sections that have been successfully processed for routine Nissl, myelin staining, DAB histochemistry, and fluorescence. The method is also suitable for larger brains, such as rat and monkey

Frequency-selective control of cortical and subcortical networks by central thalamus

Central thalamus plays a critical role in forebrain arousal and organized behavior. However, network-level mechanisms that link its activity to brain state remain enigmatic. Here, we combined optogenetics, fMRI, electrophysiology, and video-EEG monitoring to characterize the central thalamus-driven global brain networks responsible for switching brain state. 40 and 100 Hz stimulations of central thalamus caused widespread activation of forebrain, including frontal cortex, sensorimotor cortex, and striatum, and transitioned the brain to a state of arousal in asleep rats. In contrast, 10 Hz stimulation evoked significantly less activation of forebrain, inhibition of sensory cortex, and behavioral arrest. To investigate possible mechanisms underlying the frequency-dependent cortical inhibition, we performed recordings in zona incerta, where 10, but not 40, Hz stimulation evoked spindle-like oscillations. Importantly, suppressing incertal activity during 10 Hz central thalamus stimulation reduced the evoked cortical inhibition. These findings identify key brain-wide dynamics underlying central thalamus arousal regulation

Constructing isosurfaces in a localized fashion using an underlying octree data structure

We present an octree-based approach for isosurface extraction from large volumetric scalar-valued data. Given scattered points with associated function values, we impose an octree structure of relatively low resolution. Octree construction is controlled by original data resolution and cell-specific error values. For each cell in the octree, we compute an average function value and additional statistical data for the original points inside the cell. Once a specific isovalue is specified, we adjust the initial octree by expanding its leaves based on a comparison of statistics with the isovalue. We tetrahedrize the centers of the octree's cells to determine tetrahedral meshes decomposing the entire spatial domain of the data, including a possibly specific region of interest (ROI). Extracted isosurfaces are crack-free inside an ROI, but cracks can appear at the boundary of an ROI. The inital isosurface is an approximation of the exact one, but its quality suffices for a viewer to identify an ROI where more accuracy is desirable. In the refinement process, we refine affected octree nodes and update the triangulation locally to produce better isosurface representations. This adaptive and user-driven refinement provides a means for interactive data exploration via real-time and local isosurface extraction

An octree-based multiresolution approach supporting interactive rendering of very large volume data sets

We present an octree-based approach supporting multiresolution volume rendering of large data sets. Given a set of scattered points without connectivity information, we impose an actree data structure of low resolution in the preprocessing step. The construction of this initial octree structure of low resolution in the preprocessing step. The construction of this initial octree structure is controlled by the original data resolution and cell-specific error values. Using the octree nodes, rather than the data points, as elementary units for ray casting, we first generate a crude rendering of a given data set. Keeping the pre-processing step independent from the rendering step, we allow a user to interactively explore a large data set by speicifying a region of interest (ROI), where a higher level of rendering accuracy is desired. To refine an ROI, we are making use of the octree constructed in the pro-processing step. Our approach is aimed at minimizing the number of computations and can be applied to large-scale data exploration tasks

A low-cost technique to cryo-protect and freeze rodent brains, precisely aligned to stereotaxic coordinates for whole-brain cryosectioning

A major challenge in the histological sectioning of brain tissue is achieving accurate alignment in the standard coronal, horizontal, or sagittal planes. Correct alignment is desirable for ease of subsequent analysis and is a prerequisite for computational registration and algorithm-based quantification of experimental data. We have developed a simple and low-cost technique for whole-brain cryosectioning of rodent brains that reliably results in a precise alignment of stereotactic coordinates. The system utilises a 3-D printed model of a mouse brain to create a tailored cavity that is used to align and support the brain during freezing. The alignment of the frozen block is achieved in relation to the fixed edge of the mould. The system also allows for two brains to be frozen and sectioned simultaneously. System components, procedural steps, and examples of the end results are presented

Octree Data Structure for Large-Scale

The fields of medical imaging, vector field visualization, flow simulation, and computational fluid dynamics (CFD) produce large data sets. These datasets cannot be rendered in a reasonable amount of time. Rendering a complete data set at high resolution is often timeconsumin

A Hierarchical Error-Controlled Octree Data Structure for Large-Scale Visualization

We present an octree-based approach supporting multiresolution visualization of large three-dimenstional scientific data sets. Given an irregular gridded data set, we initially impose an octree data structure of relatively low resolution, i.e., consisting of a relatively small number of cells. The construction of this initial octree structure is controlled by the original data resolution and cell-specific error value. It is thus possible to use the octree to visualize either the field function value or the local error value. The octreee data structure can be refined further in areas that are specified by a user of a visualization system: A user would identify a region in space, i.e., an octree cell, where the field is of greater interest or where octree cells carry relatively large error values. This usage of our data sturcture ensures that we use the highest resolution to render only regions of interest in a large-scale scientific data set

The active atlas: Combining 3D anatomical models with texture detectors

While modern imaging technologies such as fMRI have opened exciting possibilities for studying the brain in vivo, histological sections remain the best way to study brain anatomy at the level of neurons. The procedure for building histological atlas changed little since 1909 and identifying brain regions is a still a labor intensive process performed only by experienced neuroanatomists. Existing digital atlases such as the Allen Reference Atlas are constructed using downsampled images and can not reliably map low-contrast parts such as brainstem, which is usually annotated based on high-resolution cellular texture. We have developed a digital atlas methodology that combines information about the 3D organization and the detailed texture of different structures. Using the methodology we developed an atlas for the mouse brainstem, a region for which there are currently no good atlases. Our atlas is “active” in that it can be used to automatically align a histological stack to the atlas, thus reducing the work of the neuroanatomist. © 2017, Springer International Publishing AG