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  1. .. module:: neo
  2. .. image:: images/neologo.png
  3. :width: 600 px
  4. Neo is a Python package for working with electrophysiology data in Python, together
  5. with support for reading a wide range of neurophysiology file formats, including
  6. Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, Igor Pro, and support for
  7. writing to a subset of these formats plus non-proprietary formats including Klustakwik and HDF5.
  8. The goal of Neo is to improve interoperability between Python tools for
  9. analyzing, visualizing and generating electrophysiology data, by providing a common,
  10. shared object model. In order to be as lightweight a dependency as possible,
  11. Neo is deliberately limited to represention of data, with no functions for data
  12. analysis or visualization.
  13. Neo is used by a number of other software tools, including OpenElectrophy_
  14. and SpykeViewer_ (data analysis and visualization), Elephant_ (data analysis),
  15. the G-node_ suite (databasing) and PyNN_ (simulations).
  16. Neo implements a hierarchical data model well adapted to intracellular and
  17. extracellular electrophysiology and EEG data with support for multi-electrodes
  18. (for example tetrodes). Neo's data objects build on the quantities_ package,
  19. which in turn builds on NumPy by adding support for physical dimensions. Thus
  20. Neo objects behave just like normal NumPy arrays, but with additional metadata,
  21. checks for dimensional consistency and automatic unit conversion.
  22. A project with similar aims but for neuroimaging file formats is `NiBabel`_.
  23. Documentation
  24. -------------
  25. .. toctree::
  26. :maxdepth: 1
  27. install
  28. core
  29. usecases
  30. io
  31. examples
  32. api_reference
  33. whatisnew
  34. developers_guide
  35. io_developers_guide
  36. authors
  37. License
  38. -------
  39. Neo is free software, distributed under a 3-clause Revised BSD licence (BSD-3-Clause).
  40. Support
  41. -------
  42. If you have problems installing the software or questions about usage, documentation or anything
  43. else related to Neo, you can post to the `NeuralEnsemble mailing list`_. If you find a bug,
  44. please create a ticket in our `issue tracker`_.
  45. Contributing
  46. ------------
  47. Any feedback is gladly received and highly appreciated! Neo is a community project,
  48. and all contributions are welcomed - see the :doc:`developers_guide` for more information.
  49. `Source code <https://github.com/NeuralEnsemble/python-neo>`_ is on GitHub.
  50. .. _OpenElectrophy: https://github.com/OpenElectrophy/OpenElectrophy
  51. .. _Elephant: http://neuralensemble.org/elephant
  52. .. _G-node: http://www.g-node.org/
  53. .. _Neuroshare: http://neuroshare.org/
  54. .. _SpykeViewer: https://spyke-viewer.readthedocs.org/en/latest/
  55. .. _NiBabel: http://nipy.sourceforge.net/nibabel/
  56. .. _PyNN: http://neuralensemble.org/PyNN
  57. .. _quantities: http://pypi.python.org/pypi/quantities
  58. .. _`NeuralEnsemble mailing list`: http://groups.google.com/group/neuralensemble
  59. .. _`issue tracker`: https://github.com/NeuralEnsemble/python-neo/issues