Atlas Viewer for the Allen Institute Common Coordinate Framework

Features

• Display CCF atlas data sliced at arbitrary angles
• Color atlas regions based on their anatomical labels or by cortical layer
• Displays anatomical label of the atlas region under the mouse pointer
• Reusable PyQt widgets can be embedded into existing GUIs

The viewer downloads three pieces of data from the Allen Institute website:

• Atlas data: http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/average_template/
• Label data: http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2015/
• Ontology: http://api.brain-map.org/api/v2/structure_graph_download/1.json

More information about the atlas data and ontology files is available at:

• http://help.brain-map.org/display/mouseconnectivity/API#API-DownloadAtlas
• http://help.brain-map.org/display/api/Downloading+an+Ontology%27s+Structure+Graph
• http://help.brain-map.org/display/api/Atlas+Drawings+and+Ontologies#AtlasDrawingsandOntologies-StructuresAndOntologies

Requirements

• Python 3+
• PyQt5
• PyQtGraph
• numpy
• nrrd
• h5py

Running the application

Start the viewer from the command prompt:

$ python viewer.py

The first time the viewer runs, it will download atlas data from the Allen Institute website. Data is then converted into a format that is more memory- and processor-efficient; this process can take several minutes depending on the resolution of the atlas/label files you select.

Setup

Optionally, the package can be installed to make its functionality available to other applications

$ python setup.py install