Spacipy documentation

Spacipy is collection of in-house python modules, targeted at the stereo-seq, that aims to make basic data analysis, modeling and visualization easier. It builds on the well-known NumPy, Pandas and MatPlotLib packages.

  • Quickly obtain data

  • Easily convert format

  • Create well formatted plots

  • Change coordinates effortlessly

Note

You may need to be familiar with some image processing like crop, segment to use some modules.

Quick start

Tutorial

API

  • Gem: object constructed based on pandas.DataFrame with adapted method for stereo-seq GEM file.

  • Stoarr: numpy.ndarray view casting with adapted method for spatial matrix

  • /mipplot: MIP plot