- RMA query to fetch meta-information 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
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.
To avoid possible bias introduced by using a single specimen as a registration target, the Nissl-based 3-D reference volume was not directly used. Instead, a large number of brains were mapped in advanced and averaged to form the registration target. This averaged template maybe updated periodically to include more brain specimens and is available for download as an unsigned 16-bit grayscale volume through this link.
Informatics Data Processing
The informatics data processing pipeline produces results that enable the navigation, analysis and visualization. The pipeline consists of the following components:
- an annotated 3-D reference space,
- an alignment module,
- an projection detection module,
- an projection gridding module, and
- a structure unionizer module.
The output of the pipeline is quantified projection 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 correlative search service and to support visualization of spatial relationships. See the informatics processing whitepaper for more details.
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.
See the atlas drawings and ontologies page for more information.
To avoid possible bias introduced by using a single specimen as a registration target, the Nissl-based 3-D reference volume was not directly used. Instead, a large number of brains were mapped in advanced and averaged to form the registration target. This averaged template maybe updated periodically to include more brain specimens and is available for download.
All SectionDataSets are registered to ReferenceSpace id = 9 in PIR orientation (+x = posterior, +y = inferior, +z = right).
Figure: The common reference space is in PIR orientation where x axis = Anterior-to-Posterior, y axis = Superior-to-Inferior and z axis = Left-to-Right.
3-D annotation volumes were updated in the June 2013 release to reflect changes in the atlas drawings and ontology. Also note that the volumes are now in a 32-bit format to large structure identifiers.
Three volumetric data files are available for download:
- atlasVolume: uchar (8bit) grayscale Nissl volume of the reconstructed brain at 25 µm resolution.
- annotation: uint (32bit) structural annotation volume at 25 µm resolution. The value represents the ID of the finest level structure annotated for the voxel. Note: the 3-D mask for any structure is composed of all voxels annotated for that structure and all of its descendents in the structure hierarchy.
- gridAnnotation - 200 µm: uint (32bit) structural annotation volume at grid (200 µm) resolution for gene expression analysis.
Volumetric data is stored in an uncompressed format with a simple text header file in MetaImage format.
As with gene expression SectionDataSets, 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.