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Simple application for viewing and slicing AI common coordinate framework atlas data

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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:

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

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

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Simple application for viewing and slicing AI common coordinate framework atlas data

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