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. 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. See the informatics processing whitepaper for more details. The grid level data are used downstream to provide a differential and correlative gene search service and to support visualization of spatial relationships.
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 pipeline consists of the following components: The informatics data processing pipeline produces results that enable the navigation, analysis and visualization. Figure: Experiment detail page of a sagittal SectionDataSet (id=69782969) for gene Pdyn showing meta-information, images and computed structure expression graph.
See the image download page to learn how to download images at different resolutions and regions of interest. All displayed information, images and structural expression values are also available through the API. In the web application, images from the experiment are visualized in an experiment detail page.
The left side of a coronal SectionImage corresponds to the left hemisphere.Ī 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.įrom the API, detailed information about Genes, Probes, SectionDataSets and SectionImages can be obtained using RMA queries.
A coronal SectionDataSet spans both hemispheres starting with the most posterior section showing the cerebellum and hindbrain to the most anterior section showing the olfactory bulb, yielding ~60 SectionImages at 200 µm sampling density. A sagittal SectionDataSet spans the left hemisphere starting with the most lateral section located at where the hippocampus starts to appear to just past the midline yielding ~20 SectionImages at 200 µm sampling density. A subset of genes also has a coronal SectionDataSet and/or replicate experiments. Typically, the sectioning scheme divided each brain into eight interleaving SectionDataSets with 200 µm sampling density (= 8 x 25 µm thickness).Įach gene was assayed with at least one sagittal SectionDataSet. Multiple genes were assayed using each Specimen. Experimental Overview And MetadataĮxperimental data from this atlas is associated with the "Mouse Brain" Product. See the main API documentation for more information on data models and query syntax. API database object names are in camel case. This document provides a brief overview of the data, database organization and example queries. Each data set is processed through an informatics analysis pipeline to obtain spatially mapped quantified expression information.ĭownload images Download quantified expression values by structure Download quantified expression values as 3-D grids Query the differential and correlative search services Query the image synchronization service Download atlas images, drawings and structure ontology The Allen Mouse Brain Atlas provides genome-wide in situ hybridization (ISH) image data for approximately 20,000 genes in adult mice.