Allen Institute Notes

Allen SDK

• install guide
• main repo
• Docs
  • Visual coding - neuropixels: Ephys experiment where animals were passively watching. summary and tutorial links
  • Visual behavior - neuropixels: Ephys experiment where animals were performing a task. summary and tutorial links
• legacy example nbs
• data access tutorial

Resources

• Blog post about Allen data and use of Xarray
• GitHub > AllenNeuralDynamics/aind-ephys-utils. This is mentioned in the blog post above as their in-progress work to create more ephys software tools
• Very high level summary of visual coding efforts
• 2022 summer workshop materials
• Community forum

Data

• Registry of Open Data on AWS - Allen Brain Observatory - Visual Coding AWS Public Data Set

Notebooks of interest (in progress)

• https://allensdk.readthedocs.io/en/latest/_static/examples/nb/ecephys_session.html
• TODO: Look up how this works: from allensdk.brain_observatory.ecephys.visualization import raster_plot
• https://allensdk.readthedocs.io/en/latest/_static/examples/nb/ecephys_quickstart.html

Other

• They are using Zarr storage for their exa-spim data (2 GB/s)