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A manual QC protocol defines the criteria for failing experiments due to production issues, discarding damaged SectionImages, verifying and adjusting the tissue bounding boxes, as well as for identifying "dark" artifacts such as bubbles and tears.

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DownloadImages
DownloadImages

From the API, detailed information about Genes, Probes, SectionDataSets and SectionImages can be obtained using RMA queries.

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From the above query, gene Pdyn has one sagittal SectionDataSet (id=69782969) and one coronal SectionDataSet (id=71717084). In the web application, images from the experiment are visualized in an experiment detail page. All displayed information, images and structural expression values are also available through the API.

AnchorDownloadImagesDownloadImages See the image download page to learn how to download images at different resolutions and regions of interest.

Figure: Experiment detail page of a sagittal SectionDataSet (id=69782969) for gene Pdyn showing meta-information, images and computed structure expression graph.

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The output of the pipeline is quantified expression 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 a differential and correlative gene search service and to support visualization of spatial relationships. See the informatics processing whitepaper for more details.

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DownloadAtlas
DownloadAtlas
3-D Reference Models

The backbone of the automated pipeline is an annotated 3-D reference space based on the same Specimen used for the coronal plates of the integrated reference atlas. A brain volume was reconstructed from the SectionImages using a combination of high frequency section-to-section histology registration with low-frequency histology to (ex-cranio) MRI registration. This first-stage reconstructed volume was then aligned with a sagittally sectioned Specimen. Once a straight mid-sagittal plane was achieved, a synthetic symmetric space was created by reflecting one hemisphere to the other side of the volume.

Over 800 Structures were extracted from the 2-D coronal reference atlas plates and interpolated to create symmetric 3-D annotations. Structures in the reference atlas are arranged in a hierarchical organization. Each structure has one parent and denotes a "part-of" relationship. Structures are assigned a color to visually emphasize their hierarchical positions in the brain.

 AnchorDownloadAtlasDownloadAtlas See the atlas drawings and ontologies page for more information.

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