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API:
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Mouse
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Connectivity
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Resources
| Table of Contents |
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Mouse Connectivity Projection Data: Informatics Data Processing Pipeline
The primary data of the Allen Mouse Brain Connectivity Atlas consists of high-resolution images of axonal projections targeting different anatomic regions or various cell types using Cre-dependent specimens. The informatics data processing pipeline produces results that enable the navigation, analysis and visualization of this data.
The output of the pipeline is quantified signal values at a grid voxel level and at a structure level according to the integrated reference atlas ontology. The grid level data are used downstream to provide an on-the-fly data and search service and to support visualization of spatial relationships.
Refer to the informatics whitepaper for detailed methods used in the pipeline.
Mouse Connectivity Projection Experiments
Experimental data from the Atlas is associated with the "Mouse Connectivity Projection" Product.
Each Specimen is injected with a viral tracer that labels axons by expressing a fluorescent protein. For each experiment, the injection site is analyzed and assigned a primary injection structure and if applicable a list of secondary injection structures.
Labeled axons are visualized using serial two-photon tomography. A typical dataset consists of 140 coronal images at 100 µm sampling density. Each image has 0.35 µm pixel resolution and raw data is in 16-bit per channel format.
From the API, detailed information about images, injection annotation and transgenic lines can be obtained using RMA queries.
Examples:
- All experiments in the "Mouse Connectivity Projection" Product
- All experiments with injection in the primary visual area (VISp, structure_id=385)
- Detailed metadata for one experiment with injection in the VISp (id=126862385) (http://iwarehouse/api/v2/data/query.xml?criteria=model::SectionDataSet,rma::criteria,
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- %5Bid$eq126862385%5D,rma::include,specimen(injections(
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- structure%5Bid$eq385%5D)),equalization,sub_images,rma::options%5Border$eq'sub_images.section_number$asc'%5D
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- )
Figure: Projection dataset (id=126862385)
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with
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injection
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in
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the
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primary
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visual
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area
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(VISp)
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as
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visualized
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in
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the
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web
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application
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image
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viewer.
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To
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provide
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a
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uniform
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look
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over
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all
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experiments,
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default
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window
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and
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level
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values
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were
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computed
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using
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intensity
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histograms.
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For
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each
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experiment,
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the
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upper
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threshold
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defaults
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to
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(2.33
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x
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the
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95th
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percentile
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value)
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for
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the
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red
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channel
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and
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(6.33
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x
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the
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95th
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percentile
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value)
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for
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the
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green
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channel.
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The
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default
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threshold
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can
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be
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used
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to
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download
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images
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and/or
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image
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region
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in
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8-bit
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per
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channel
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image
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format.
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Examples:
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- of one projection image
- Download image downsampled by factor of 6 using default thresholds
- Download a region of interest at full resolution using default thresholds
3-D Reference Model for Mouse Connectivity
| Wiki Markup |
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The backbone of the automated pipeline is an annotated 3-D reference space. Similarly to gene expression data in the [Allen Mouse Brain Atlas|http://mouse.brain-map.org/], each projection dataset is registered to the \[3-D reference space\](#3-D_Reference_Models) built upon the coronal [Allen Reference Atlas|http://mouse.brain-map.org/static/atlas] specimen. |
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To
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avoid
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possible
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bias
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introduced
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by
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using
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a
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single
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specimen
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as
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a
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registration
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target,
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the
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Nissl-based
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3-D
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reference
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volume
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was
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not
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directly
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used.
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Instead,
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a
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large
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number
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of
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brains
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were
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mapped
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in
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advanced
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and
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averaged
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to
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form
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the
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registration
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target.
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This
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averaged
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template
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maybe
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updated
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periodically
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to
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include
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more
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brain
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specimens
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and
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is
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available
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for
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download
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as
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an
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unsigned
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16-bit
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grayscale
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volume
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through
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this
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.
As with gene expression datasets, an image synchronization service is available to find corresponding position between datasets within the Mouse Connectivity Projection product and across to datasets in the Mouse Brain and Developing Mouse Brain products.
Figure: Point-based image synchronization. Multiple image-series in the Zoom-and-Pan (Zap) viewer can be synchronized to the same approximate location. Before and after synchronization screenshots show projection data with injection in the superior colliculus (SCs), primary visual area (VISp) anteolateral visual area (VISal), and the relevant coronal plates of the Allen Reference Atlas. All experiments show strong signal in the thalamus.
Projection Data Segmentation
For every Projection image, a gray scale mask is generated that identifies pixels corresponding to labeled axon trajectories. The segmentation algorithm is based on image edge/line detection and morphological filtering. The segmentation mask image is the same size and pixel resolution as the primary projection image and can be downloaded.
Figure: Signal detection for projection data with injection in the primary motor area. Screenshot of a segmentation mask showing detected signal in the ventral posterolateral nucleus of the thalamus (VPL), internal capsule (int), caudoputamen (CP) and supplemental somatosensory area (SSs). In the Web application, the mask is color-coded for display: green indicates a pixel is part of an edge-like object while yellow indicates pixels that are part of a more diffuse region.
Projection Data Gridding
For each dataset, the gridding module creates a low resolution 3-D summary of the labeled axonal trajectories and resamples the data to the common coordinate space of the 3-D reference model. Casting all data into a canonical space allows for easy cross-comparison between datasets. The projection data grids can also be viewed directly as 3-D volumes or used for analysis (i.e. afferent and correlative searches).
Each image in a dataset is divided into a 100 x 100 µm grid. Pixel-based statistics are computed using information from the primary image and the segmentation mask:
- projection density = sum of detected pixels / sum of all pixels in division
- projection intensity = sum of detected pixel intensity / sum of detected pixels
- projection energy = projection intensity * projection density
| Wiki Markup |
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The resulting 3-D grid is then transformed into the standard reference space. Grid data can be downloaded for each SectionDataSet using the \[3-D Grid Data Service\](/doc/index.html#Downloading_3-D_Expression_Grid_Data). The service returns a zip file containing the volumetric data for density, intensity and/or energy in an uncompressed format with a simple text header file in [MetaImage|http://www.itk.org/Wiki/MetaIO/Documentation] format. Structural annotation for each grid voxel can be obtained via the ReferenceSpace [gridAnnotation|http://iwarehouse/api/v2/well_known_file_download/159081322] volume file at 100 µm grid resolution. |
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Examples:
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Example Matlab code snippet to read in the 100 µm density grid volume:
% Download and unzip the density grid file for VISp SectionDataSet
| Wiki Markup |
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<span |
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style="color: #339966 |
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">% 100 micron volume |
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size</span> sizeGrid = \[133 81 115\]; |
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<span style="color: #339966 |
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">% DENSITY = 3-D matrix of projection density grid |
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volume</span> fid = fopen('density.raw', 'r', 'l' ); DENSITY = fread( fid, prod(sizeGrid), 'float' ); fclose( fid ); DENSITY = reshape(DENSITY,sizeGrid) |
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; |
| Wiki Markup |
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|
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<span style="color: #339966 |
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">% Display one coronal and one sagittal |
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section</span> figure;imagesc(squeeze(DENSITY (95,:,\:)));caxis(\[0,1\]);colormap(hot); figure;imagesc(squeeze(DENSITY (:,:,72)));caxis(\[0,1\]);colormap(hot); |
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Projection
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Structure
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Unionization
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Projection
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signal
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statistics
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can
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be
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computed
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for
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each
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structure
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delineated
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in
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the
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reference
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atlas
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by
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combining
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or
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unionizing
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grid
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voxels
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with
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the
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same
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3-D
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structural
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label.
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While
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the
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reference
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atlas
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is
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typically
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annotated
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at
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the
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lowest
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level
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of
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the
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ontology
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tree,
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statistics
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at
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upper
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level
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structures
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can
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be
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obtained
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by
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combining
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measurements
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of
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the
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hierarchical
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children
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to
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obtain
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statistics
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for
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the
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parent
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structure.
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The
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unionization
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process
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also
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separates
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out
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the
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left
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versus
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right
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hemisphere
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contributions
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as
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well
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as
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the
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injection
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versus
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non-injection
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components.
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Projection
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statistics
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are
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encapsulated
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as
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a
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object
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associated
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with
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one
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,
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either
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left,
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right
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or
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both
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Hemispheres
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and
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one
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.
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Example:
| Wiki Markup |
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Download structure projection signal statistics for one VISp injection experiment exclusive of injection area\](/api/v2/data/ProjectionStructureUnionize/query.xml?criteria=\[section_data_set_id$eq126862385\],\[is_injection$eqfalse\]&num_rows=5000&include=structure)
\* \[Download injection site statistics for the same experiment\](/api/v2/data/ProjectionStructureUnionize/query.xml?criteria=\[section_data_set_id$eq126862385\],\[is_injection$eqtrue\]&num_rows=5000&include=structure) |
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ProjectionStructureUnionize
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data
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is
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used
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in
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the
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web
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application
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to
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display projection summary bar graphs.
<a href="#"
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onmouseover="hover"
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title="Back
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to
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top"><img
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width="18px"
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height="20px"
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src="/images/back_to_top.png"
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/></a>
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###
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Comparing
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Projection
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Data
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Grids
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and
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Gene
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Expression
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Grids
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Due
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to
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section
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sampling
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density,
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projection
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data
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grids
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are
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at
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100µm
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resolution
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while
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gene
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expression
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grids
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are
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at
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200µm
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resolution.
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Upsampling
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with
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appropriate
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interpolation
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of
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the
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gene
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expression
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data
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is
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necessary
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in
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order
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to
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numerically
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compare
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between
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the
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two
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different
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types
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of
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data.
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When
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interpolating
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the
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data,
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"no
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data"
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(-1)
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voxels
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needs
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to
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be
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handled
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specifically.
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Example
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Matlab
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code
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snippet
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to
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upsample
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gene
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expression
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grid
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with
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"no
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data"
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handling:
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% Download and unzip energy volume file for gene Rasd2 coronal SectionDataSet 73636089
mkdir('Rasd2_73636089');
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urlwrite('http://api.brain-map.org/grid_data/download/74819249?include=density',
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'temp.zip');
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unzip('temp.zip','Rasd2_
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73636089');
% Download and unzip density volume file for BLAa injection SectionDataSet 113144533
mkdir('BLAa_113144533');
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urlwrite('http://api.brain-map.org/grid_data/download/113144533?include=density',
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'temp.zip');
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unzip('temp.zip','BLAa_113144533')
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;
| Wiki Markup |
|---|
% Gene expression grids are at 200 micron resolution.
geneGridSize = \[67 41 58\];
fid = fopen('Rasd2_73636089/density.raw', 'r', 'l' );
Rasd2 = fread( fid, prod(geneGridSize), 'float' );
fclose(fid);
Rasd2 = reshape( Rasd2, geneGridSize ); |
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| Wiki Markup |
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% Projection grids are at 100 micron resolution
projectionGridSize = \[133 81 115\];
fid = fopen('BLAa_113144533/density.raw', 'r', 'l' );
BLAa = fread( fid, prod(projectionGridSize), 'float' );
fclose(fid);
BLAa = reshape( BLAa, projectionGridSize ); |
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| Wiki Markup |
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% Upsample gene expression grid to same dimension as projection grid using linear interpolation
\[xi,yi,zi\] = meshgrid(1:0.5:41,1:0.5:67,1:0.5:58); %note: matlab transposes x-y
d = Rasd2; d(d<0) = 0; % fill in missing data as zeroes
Rasd2_100 = interp3(d ,xi,yi,zi,'linear'); |
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% Handle "no data" (-1)
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voxels.
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% Create a mask of "data"
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vs
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"no
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data"
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voxels
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and
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apply
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linear
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interpolation
m = (Rasd2 >= 0);
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mi
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=
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interp3(m,xi,yi,zi,'linear');
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% Normalize data by dividing by interpolated mask. Assign value of "-1"
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to
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"no data" voxels.
Rasd2_100
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=
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Rasd2_100
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./
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mi;
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Rasd2_100(
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mi
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<=
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0
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)
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=
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-1;
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| Wiki Markup |
|---|
% Create a merged image of one coronal plane;
gimg = squeeze(Rasd2_100(52,:,\:)); gimg = max(0,gimg); gimg = gimg / 0.025; gimg = min(1,gimg);
pimg = squeeze(BLAa(52,:,\:)); pimg = max(0,pimg); pimg = pimg / 0.8; pimg = min(1,pimg);
rgb = zeros(\[size(gimg),3\]); rgb(:,:,1) = gimg; rgb(:,:,2) = pimg;
figure; image(rgb); |
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<img
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width="800px"
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src="/images/UpsampleGeneExpressionGrid.jpg"
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/>
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*Figure:
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*
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ISH
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SectionDataSet
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(id=73636089)
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for
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gene
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Rasd2
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showing
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enriched
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expression
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in
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the
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striatum
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(left).
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Projection
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SectionDataSet
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(id=73636089)
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with
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injection
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in
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the
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anterior
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part
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of
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the
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basolateral
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amygdalar
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nucleus
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(BLAa)
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showing
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projection
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to
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the
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striatum
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and
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other
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brain
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areas
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(center).
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One
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coronal
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slice
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of
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the
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BLAa
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projection
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density
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grid
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(green)
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merged
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with
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an
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upsampled
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and
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interpolated
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Rasd2
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expression
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density
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grid
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(red).
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<a
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href="#"
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onmouseover="hover"
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title="Back
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to
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top"><img
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width="18px"
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height="20px"
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src="/images/back_to_top.png"
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/></a>