The Cre/lox system is widely used in mice to achieve cell-type-specific gene expression. However, a strong and universally responding system to express genes under Cre control is still lacking. We ...have generated a set of Cre reporter mice with strong, ubiquitous expression of fluorescent proteins of different spectra. The robust native fluorescence of these reporters enables direct visualization of fine dendritic structures and axonal projections of the labeled neurons, which is useful in mapping neuronal circuitry, imaging and tracking specific cell populations in vivo. Using these reporters and a high-throughput in situ hybridization platform, we are systematically profiling Cre-directed gene expression throughout the mouse brain in several Cre-driver lines, including new Cre lines targeting different cell types in the cortex. Our expression data are displayed in a public online database to help researchers assess the utility of various Cre-driver lines for cell-type-specific genetic manipulation.
Recent large-scale collaborations are generating major surveys of cell types and connections in the mouse brain, collecting large amounts of data across modalities, spatial scales, and brain areas. ...Successful integration of these data requires a standard 3D reference atlas. Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 μm z-sampling from 1,675 young adult C57BL/6J mice. Then, using multimodal reference data, we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures. CCFv3 can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D and is openly accessible (https://atlas.brain-map.org/).
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•Created a 3D average template brain from 1,675 mice at 10-μm voxel resolution•Delineated 43 isocortical areas from multiple surface views using curved coordinates•Delineated 329 subcortical areas, 8 ventricle structures, and 81 fiber tracts in 3D•The Allen CCF is open access and available with related tools at https://atlas.brain-map.org/
The Allen Mouse Brain CCF is an openly accessible, cellular level resolution 3D reference atlas for analysis, visualization, and integration of multimodal and multiscale datasets.
Significant advances in circuit-level analyses of the brain require tools that allow for labeling, modulation of gene expression, and monitoring and manipulation of cellular activity in specific cell ...types and/or anatomical regions. Large-scale projects and individual laboratories have produced hundreds of gene-specific promoter-driven Cre mouse lines invaluable for enabling genetic access to subpopulations of cells in the brain. However, the potential utility of each line may not be fully realized without systematic whole brain characterization of transgene expression patterns. We established a high-throughput in situ hybridization (ISH), imaging and data processing pipeline to describe whole brain gene expression patterns in Cre driver mice. Currently, anatomical data from over 100 Cre driver lines are publicly available via the Allen Institute's Transgenic Characterization database, which can be used to assist researchers in choosing the appropriate Cre drivers for functional, molecular, or connectional studies of different regions and/or cell types in the brain.
The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful ...search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.
Purpose
Mobile lung tumors are increasingly being treated with ablative radiotherapy, for which precise motion management is essential. In‐room stereoscopic radiography systems are able to guide ...ablative radiotherapy for stationary cranial lesions but not optimally for lung tumors unless fiducial markers are inserted. We propose augmenting stereoscopic radiographic systems with multiple small x‐ray sources to provide the capability of imaging with stereoscopic, single frame tomosynthesis.
Methods
In single frame tomosynthesis, nine x‐ray sources are placed in a 3 × 3 configuration and energized simultaneously. The beams from these sources are collimated so that they converge on the tumor and then diverge to illuminate nine non‐overlapping sectors on the detector. These nine sector images are averaged together and filtered to create the tomosynthesis effect. Single frame tomosynthesis is intended to be an alternative imaging mode for existing stereoscopic systems with a field of view that is three times smaller and a temporal resolution equal to the frame rate of the detector. We simulated stereoscopic tomosynthesis and radiography using Monte Carlo techniques on 60 patients with early‐stage lung cancer from the NSCLC‐Radiomics dataset. Two board‐certified radiation oncologists reviewed these simulated images and rated them on a 4‐point scale (1: tumor not visible; 2: tumor visible but inadequate for motion management; 3: tumor visible and adequate for motion management; 4: tumor visibility excellent). Each tumor was independently presented four times (two viewing angles from radiography and two viewing angles from tomosynthesis) in a blinded fashion over two reading sessions.
Results
The fraction of tumors that were rated as adequate or excellent for motion management (scores 3 or 4) from at least one viewing angle was 53% using radiography and 90% using tomosynthesis. From both viewing angles, the corresponding fractions were 7% for radiography and 48% for tomosynthesis. Readers agreed exactly on 62% of images and within 1 point on 98% of images. The acquisition technique was estimated to be 75 mAs at 120 kVp per treatment fraction assuming one verification image per breath, approximately one order of magnitude less than a standard dose cone beam CT.
Conclusions
Stereoscopic tomosynthesis may provide a noninvasive, low dose, intrafraction motion verification technique for lung tumors treated by ablative radiotherapy. The system architecture is compatible with real‐time video capture at 30 frames per second. Simulations suggest that most, but not all, lung tumors can be adequately visualized from at least one viewing angle.
The mammalian cortex is a laminar structure containing many areas and cell types that are densely interconnected in complex ways, and for which generalizable principles of organization remain mostly ...unknown. Here we describe a major expansion of the Allen Mouse Brain Connectivity Atlas resource
, involving around a thousand new tracer experiments in the cortex and its main satellite structure, the thalamus. We used Cre driver lines (mice expressing Cre recombinase) to comprehensively and selectively label brain-wide connections by layer and class of projection neuron. Through observations of axon termination patterns, we have derived a set of generalized anatomical rules to describe corticocortical, thalamocortical and corticothalamic projections. We have built a model to assign connection patterns between areas as either feedforward or feedback, and generated testable predictions of hierarchical positions for individual cortical and thalamic areas and for cortical network modules. Our results show that cell-class-specific connections are organized in a shallow hierarchy within the mouse corticothalamic network.
Visual perception and behavior are mediated by cortical areas that have been distinguished using architectonic and retinotopic criteria. We employed fluorescence imaging and GCaMP6 reporter mice to ...generate retinotopic maps, revealing additional regions of retinotopic organization that extend into barrel and retrosplenial cortices. Aligning retinotopic maps to architectonic borders, we found a mismatch in border location, indicating that architectonic borders are not aligned with the retinotopic transition at the vertical meridian. We also assessed the representation of visual space within each region, finding that four visual areas bordering V1 (LM, P, PM and RL) display complementary representations, with overlap primarily at the central hemifield. Our results extend our understanding of the organization of mouse cortex to include up to 16 distinct retinotopically organized regions.
•Full brain coverage mouse connectivity atlas.•Automated pipeline algorithms for signal detection and registration.•Web application tools for search and visualization.
The Allen Mouse Brain ...Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.
Digital reconstructions provide an accurate and reliable way to store, share, model, quantify, and analyze neural morphology. Continuous advances in cellular labeling, tissue processing, microscopic ...imaging, and automated tracing catalyzed a proliferation of software applications to reconstruct neural morphology. These computer programs typically encode the data in custom file formats. The resulting format heterogeneity severely hampers the interoperability and reusability of these valuable data. Among these many alternatives, the SWC file format has emerged as a popular community choice, coalescing a rich ecosystem of related neuroinformatics resources for tracing, visualization, analysis, and simulation. This report presents a standardized specification of the SWC file format. In addition, we introduce xyz2swc, a free online service that converts all 26 reconstruction formats (and 72 variations) described in the scientific literature into the SWC standard. The xyz2swc service is available open source through a user-friendly browser interface ( https://neuromorpho.org/xyz2swc/ui/ ) and an Application Programming Interface (API).
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