Precomputed Unit Analysis Metrics

Technical
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1

Hi,

At the bottom of this page, Visual Coding – Neuropixels — Allen SDK dev documentation it notes to use the “get_unit_analysis_metrics()” method to get metrics of global orientation selectivity, sparseness etc. Additionally, it is mentioned in the Allen SDK documentation release dev.

However, I am having trouble calling this data, as I cant find which module this is part of. I have attempted things such as:

from allensdk.brain_observatory.ecephys.ecephys_session import get_unit_analysis_metrics
from allensdk.brain_observatory.ecephys.ecephys_project_cache import get_unit_analysis_metrics
from allensdk.brain_observatory.ecephys.ecephys_project_api import get_unit_analysis_metrics
import allensdk.brain_observatory.ecephys.ecephys_project_api

I have been able to find a table for the calcium imaging data using what I assume is a similar method - “get_cell_specimens()” on this page Brain Observatory — Allen SDK dev documentation (as there is an associated jupyter notebook tutorial) but I am looking for the neuropixel data.

This may be a simple question, but I am having quite a bit of trouble and cant find any answers anywhere else, thus would appreciate any help if you know how to call the table.

2

Hello! This method belongs to the EcephysProjectCache object (the same one used to download data).

You can create the cache object like this:

from allensdk.brain_observatory.ecephys.ecephys_project_cache import EcephysProjectCache

output_dir = '/local1/ecephys_cache_dir' # customize this
manifest_path = os.path.join(output_dir, "manifest.json")
cache = EcephysProjectCache.from_warehouse(manifest=manifest_path)

Then, you can access the analysis metrics like this:

analysis_metrics1 = cache.get_unit_analysis_metrics_by_session_type('brain_observatory_1.1')

analysis_metrics2 = cache.get_unit_analysis_metrics_by_session_type('functional_connectivity')

These steps are documented in this tutorial, but we should also make this clear on the landing page!

1 Like
3

Thank you for this quick response! This is exactly what I was looking for, thank you.