BrainGlobe version 1 is here! Head over to the blog to find out more

Conventions#

Documentation#

  • We use Sphinx to generate documentation (hosted on this website), built with the PyData Sphinx Theme.

  • Docstrings should be written in numpydoc format.

  • Documentation structure should be informed by the diataxis framework.

Dependency support#

Packages have to choose which versions of dependencies they officially support, with minimum supported versions of each dependency used in continuous integration testing. BrainGlobe projects should follow NEP 29 — Recommend Python and NumPy version support as a community policy standard to determine the minimum set of supported package versions:

  • The last 42 months of Python releases

  • The last 24 months of NumPy releases

In addition to this, the last 24 months of other dependencies should also be supported.

Axis ordering in spatial arrays#

For arrays representing spatial data, we follow zyx axis ordering in the same way as numpy and napari. The origin is the upper left corner when you show the first element stack[0, :, :]. The first dimension is the one that you are slicing, the second is the height of the image, and the third is the width of the image. The brainglobe-space package provides an interface to manipulate data following different conventions to adhere to this standard.