- 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
- Python 2.7
- PyQt4
- PyQtGraph
- numpy
- nrrd
- h5py
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.
Optionally, the package can be installed to make its functionality available to other applications
$ python setup.py install