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This document provides a brief overview of the data, database organization and example queries. API database object names are camel case. See the Data Model page for more details.

Experimental Overview and Metadata

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

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

Each gene was assayed with at least one sagittal SectionDataSet. A subset of genes also has a coronal SectionDataSet and/or replicate experiments. 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 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. The left side of a coronal SectionImage corresponds to the left hemisphere.

A manual QC protocol defined 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.