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(icon) The Allen Mouse Brain Atlas provides genome-wide in situ hybridization (ISH) data for approximately 20,000 genes in adult mice. Each data set is processed through an informatics analysis pipeline to obtain spatially mapped quantified expression information.

From the API, you can:

  • (icon) Download images
  • (icon) Download quantified expression values by structure
  • (icon) Download quantified expression values as 3-D grids
  • (icon) Query the differential and correlative search services
  • (icon) Query the image synchronization service

Mouse Brain ISH Data: Informatics Data Processing Pipeline

The Allen Mouse Brain Atlas (the Atlas) provides genome-wide in situ hybridization (ISH) data for approximately 20,000 genes in male P56 C57BL/6J mice. The informatics data processing pipeline produces results that enable the navigation, analysis and visualization of this data. The informatics data processing pipeline consists of the following components:

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 an on-the-fly differential and correlative gene search service and to support visualization of spatial relationships.

Mouse Brain ISH Experiments

Experimental Metadata

Experimental data from the Atlas is associated with the "Mouse Brain" Product.

Multiple Genes genes were assayed using each Specimenspecimen. Typically, the sectioning scheme divided each brain into eight interleaving SectionDataSets with 200 µm sampling density (= 8 x 25 µm thickness).

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

Mouse Brain ISH Data: Informatics Data Processing Pipeline

The Allen Mouse Brain Atlas (the Atlas) provides genome-wide in situ hybridization (ISH) data for approximately 20,000 genes in male P56 C57BL/6J mice. The informatics data processing pipeline produces results that enable the navigation, analysis and visualization of this data. The informatics data processing pipeline consists of the following components:

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 an on-the-fly differential and correlative gene search service and to support visualization of spatial relationships.

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.

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