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Widgets for analysis of worm videos

Project description

Widgets for analyzing videos of worms.

To install, use:

setup.py install

To see other install options:

setup.py –help

In addition to the listed requirements, you will need to install wormtracker, roitools, and OpenCV, which cannot be installed from PyPI.

To install OpenCV, see http://docs.opencv.org/doc/tutorials/introduction/table_of_content_introduction/table_of_content_introduction.html.

wormtracker and roitools are by Stephen Helms and can be obtained from him (shelms@amolf.nl). wormtracker in turn requires scipy, h5py, and scikit-image, which are available from PyPI. For convenience, these are also listed as requirements of VideoAnalysis.

Other tricks to look out for: First, you will need an up-to-date version of the ipython notebook, such as 2.4. Many ipython installations have a very early version of the notebook, such as 0.x. This won’t work. You can fix this with

pip install –upgrade –user ipython

You may find, though, when you actually run ‘ipython notebook’, that it fails with the exception ‘ImportError: IPython.html requires pyzmq >= 2.1.11’. To fix this, use

pip install pyzmq

You may get a similar error for tornado, which you can also install with pip. (Why these are not listed in PyPI as requirements for ipython[notebook] I don’t understand…)

Project details


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