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API: Mouse Connectivity Resources

Table of Contents

Mouse Connectivity Projection Data: Informatics Data Processing Pipeline

Allen Brain Atlas API

Image Added The primary data of the Allen Mouse Brain Connectivity Atlas consists consists of high-resolution images of axonal projections targeting different anatomic regions or various cell types using Cre-dependent specimens. The Each data set is processed through an 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.


analysis pipeline to obtain spatially mapped quantified projection information.

From the API, you can:

Image Added Download images
Image Added Download quantified projection values by structure
Image Added Download quantified projection values as 3-D grids
Image Added Query the image synchronization service
Image Added Download atlas images, drawings and structure ontology

This document provides a brief overview of the data, database organization and example queries. API database object names are in camel case. See the main API documentation for more information on data models and query syntax.

Experimental Overview and Metadata

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


Labeled axons are visualized using serial two-photon tomography. A typical dataset SectionDataSet 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 SectionDataSets, SectionImages, Injections and TransgenicLines can be obtained using RMA queries.


Image Modified
Figure: Projection dataset (id=126862385) with injection in the primary visual area (VISp) as visualized in the web application image viewer.