Curation¶

Overview¶

Developer Note: if you may make a PR in the future, be sure to copy this notebook, and use the gitignore prefix temp to avoid future conflicts.

This is one notebook in a multi-part series on Spyglass.

• To set up your Spyglass environment and database, see this notebook
• For a more detailed introduction to DataJoint with inserts, see this notebook
• The Spike Sorting notebook is a mandatory prerequisite to Curation.

Imports¶

In [2]:

%env KACHERY_CLOUD_DIR="/home/cb/.kachery-cloud/"

%env KACHERY_CLOUD_DIR="/home/cb/.kachery-cloud/"

env: KACHERY_CLOUD_DIR="/home/cb/.kachery-cloud/"

In [6]:

import os
import warnings
import datajoint as dj

warnings.simplefilter("ignore", category=DeprecationWarning)
warnings.simplefilter("ignore", category=ResourceWarning)

# change to the upper level folder to detect dj_local_conf.json
if os.path.basename(os.getcwd()) == "notebooks":
    os.chdir("..")
dj.config.load("dj_local_conf.json")  # load config for database connection info

from spyglass.spikesorting import SpikeSorting

import os import warnings import datajoint as dj warnings.simplefilter("ignore", category=DeprecationWarning) warnings.simplefilter("ignore", category=ResourceWarning) # change to the upper level folder to detect dj_local_conf.json if os.path.basename(os.getcwd()) == "notebooks": os.chdir("..") dj.config.load("dj_local_conf.json") # load config for database connection info from spyglass.spikesorting import SpikeSorting

[2023-07-21 13:55:48,211][INFO]: Connecting root@localhost:3306
[2023-07-21 13:55:48,242][INFO]: Connected root@localhost:3306
/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/spikeinterface/sortingcomponents/peak_detection.py:643: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit(parallel=False)
/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/spikeinterface/sortingcomponents/peak_detection.py:668: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit(parallel=False)

Spikes Sorted¶

Let's check that the sorting was successful in the previous notebook.

In [9]:

# Define the name of the file that you copied and renamed from previous tutorials
nwb_file_name = "minirec20230622.nwb"
nwb_copy_file_name = "minirec20230622_.nwb"
SpikeSorting & {"nwb_file_name": nwb_copy_file_name}

# Define the name of the file that you copied and renamed from previous tutorials nwb_file_name = "minirec20230622.nwb" nwb_copy_file_name = "minirec20230622_.nwb" SpikeSorting & {"nwb_file_name": nwb_copy_file_name}

Out[9]:

nwb_file_name name of the NWB file	sort_group_id identifier for a group of electrodes	sort_interval_name name for this interval	preproc_params_name	team_name	sorter	sorter_params_name	artifact_removed_interval_list_name	sorting_path	time_of_sort in Unix time, to the nearest second
minirec20230622_.nwb	0	01_s1_first9	default_hippocampus	My Team	mountainsort4	hippocampus_tutorial	minirec20230622_.nwb_01_s1_first9_0_default_hippocampus_none_artifact_removed_valid_times	/home/cb/wrk/zOther/data/"sorting"/minirec20230622_.nwb_01_s1_first9_0_default_hippocampus_3335c236_spikesorting	1689971050

Total: 1

sortingview web app¶

As of June 2021, members of the Frank Lab can use the sortingview web app for manual curation.

In [ ]:

# ERROR: curation_feed_uri not a field in SpikeSorting

# ERROR: curation_feed_uri not a field in SpikeSorting

In [ ]:

workspace_uri = (SpikeSorting & {"nwb_file_name": nwb_copy_file_name}).fetch1(
    "curation_feed_uri"
)
print(
    f"https://sortingview.vercel.app/workspace?workspace={workspace_uri}&channel=franklab"
)

workspace_uri = (SpikeSorting & {"nwb_file_name": nwb_copy_file_name}).fetch1( "curation_feed_uri" ) print( f"https://sortingview.vercel.app/workspace?workspace={workspace_uri}&channel=franklab" )

This will take you to a workspace on the sortingview app. The workspace, which you can think of as a list of recording and associated sorting objects, was created at the end of spike sorting. On the workspace view, you will see a set of recordings that have been added to the workspace.

Clicking on a recording then takes you to a page that gives you information about the recording as well as the associated sorting objects.

Click on a sorting to see the curation view. Try exploring the many visualization widgets.

The most important is the Units Table and the Curation menu, which allows you to give labels to the units. The curation labels will persist even if you suddenly lose connection to the app; this is because the curation actions are appended to the workspace as soon as they are created. Note that if you are not logged in with your Google account, Curation menu may not be visible. Log in and refresh the page to access this feature.

Up Next¶

Next, we'll turn our attention to LFP data data.