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.gitignore
README.md
api.py
download_data.py
ontology.py
unionize.py
validate_unionize_structures.py

README.md

VisWeek 2013 Contest Scripts

Use the scripts in this repository to download the developing mouse data for the VisWeek 2013 visualization contest.

A full description of this data set can be found at the official site for the contest:

http://sciviscontest.visweek.org/2013

To download the data set, simply run:

$ python download_data.py

This will probably take multiple hours. Files will be downloaded into the current working directory with the following structure:

  • energy/ - a directory full of expression energy Meta images, one for each probe in 6 development stages chosen for this contest.
  • meta/ - a directory containing meta data on probes (data_sets.csv) and structures (structures.csv).
  • atlas/ - a directory containing reference atlas volumes, one for each developmental stage.
  • annotation/ - a directory containing grid annotation volumes, one for each developmental stage. Voxel values are structure ids.
  • structure_unionizes/ - a directory containing one CSV per probe. Each CSV contains a set of rows describing the expression energy for a probe within an entire structure.

Note: this python script has only been tested with python 2.7.2.

Note 2: there have been problems reported using this script in Cygwin. If you can avoid Cygwin, please do so.