MUA Detection¶

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 the Setup notebook.
• For additional info on DataJoint syntax, including table definitions and inserts, see the Insert Data notebook.
• Prior to running, please generate sorted spikes with the spike sorting pipeline and generate input position data with either the Trodes or DLC notebooks (1, 2, 3).

The goal of this notebook is to populate the MuaEventsV1 table, which depends SortedSpikesGroup and PositionOutput.

Imports¶

In [1]:

import datajoint as dj
from pathlib import Path

dj.config.load(
    Path("../dj_local_conf.json").absolute()
)  # load config for database connection info

from spyglass.mua.v1.mua import MuaEventsV1, MuaEventsParameters

import datajoint as dj from pathlib import Path dj.config.load( Path("../dj_local_conf.json").absolute() ) # load config for database connection info from spyglass.mua.v1.mua import MuaEventsV1, MuaEventsParameters

[2024-06-04 16:03:33,573][INFO]: Connecting denissemorales@lmf-db.cin.ucsf.edu:3306
[2024-06-04 16:03:33,619][INFO]: Connected denissemorales@lmf-db.cin.ucsf.edu:3306
OMP: Info #277: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.

Select Position Data¶

In [2]:

from spyglass.position import PositionOutput

# First, select the file of interest
nwb_copy_file_name = "mediumnwb20230802_.nwb"

# Then, get position data
trodes_s_key = {
    "nwb_file_name": nwb_copy_file_name,
    "interval_list_name": "pos 0 valid times",
    "trodes_pos_params_name": "single_led_upsampled",
}

pos_merge_id = (PositionOutput.TrodesPosV1 & trodes_s_key).fetch1("merge_id")
pos_merge_id

from spyglass.position import PositionOutput # First, select the file of interest nwb_copy_file_name = "mediumnwb20230802_.nwb" # Then, get position data trodes_s_key = { "nwb_file_name": nwb_copy_file_name, "interval_list_name": "pos 0 valid times", "trodes_pos_params_name": "single_led_upsampled", } pos_merge_id = (PositionOutput.TrodesPosV1 & trodes_s_key).fetch1("merge_id") pos_merge_id

Out[2]:

UUID('4eb59a18-045a-5768-d12e-b6473415ae1c')

Select Sorted Spikes Data¶

In [3]:

from spyglass.spikesorting.analysis.v1.group import (
    SortedSpikesGroup,
)

# Select sorted spikes data
sorted_spikes_group_key = {
    "nwb_file_name": nwb_copy_file_name,
    "sorted_spikes_group_name": "test_group",
    "unit_filter_params_name": "default_exclusion",
}

SortedSpikesGroup & sorted_spikes_group_key

from spyglass.spikesorting.analysis.v1.group import ( SortedSpikesGroup, ) # Select sorted spikes data sorted_spikes_group_key = { "nwb_file_name": nwb_copy_file_name, "sorted_spikes_group_name": "test_group", "unit_filter_params_name": "default_exclusion", } SortedSpikesGroup & sorted_spikes_group_key

Out[3]:

nwb_file_name name of the NWB file	unit_filter_params_name	sorted_spikes_group_name
mediumnwb20230802_.nwb	default_exclusion	test_group

Total: 1

Setting MUA Parameters¶

In [4]:

MuaEventsParameters()

MuaEventsParameters()

Out[4]:

mua_param_name a name for this set of parameters	mua_param_dict dictionary of parameters
default	=BLOB=

Total: 1

Here are the default parameters:

In [5]:

(MuaEventsParameters() & {"mua_param_name": "default"}).fetch1()

(MuaEventsParameters() & {"mua_param_name": "default"}).fetch1()

Out[5]:

{'mua_param_name': 'default',
 'mua_param_dict': {'minimum_duration': 0.015,
  'zscore_threshold': 2.0,
  'close_event_threshold': 0.0,
  'speed_threshold': 4.0}}

Putting everything together: create a key and populate the MuaEventsV1 table

In [6]:

mua_key = {
    "mua_param_name": "default",
    **sorted_spikes_group_key,
    "pos_merge_id": pos_merge_id,
    "detection_interval": "pos 0 valid times",
}

MuaEventsV1().populate(mua_key)
MuaEventsV1 & mua_key

mua_key = { "mua_param_name": "default", **sorted_spikes_group_key, "pos_merge_id": pos_merge_id, "detection_interval": "pos 0 valid times", } MuaEventsV1().populate(mua_key) MuaEventsV1 & mua_key

Out[6]:

mua_param_name a name for this set of parameters	nwb_file_name name of the NWB file	unit_filter_params_name	sorted_spikes_group_name	pos_merge_id	detection_interval descriptive name of this interval list	analysis_file_name name of the file	mua_times_object_id
default	mediumnwb20230802_.nwb	default_exclusion	test_group	4eb59a18-045a-5768-d12e-b6473415ae1c	pos 0 valid times	mediumnwb20230802_235KSEV39O.nwb	a93532eb-2947-4552-8877-19ea0d2dcc4f

Total: 1

Now we can use fetch1_dataframe for mua data, including start times, end times, and speed.

In [7]:

mua_times = (MuaEventsV1 & mua_key).fetch1_dataframe()
mua_times

mua_times = (MuaEventsV1 & mua_key).fetch1_dataframe() mua_times

[16:03:45][WARNING] Spyglass: Multiple classes found in stack: {'`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`mua_events_parameters`', '`mua_v1`.`__mua_events_v1`'}. Please submit a bug report with the snippet used.
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.5.1 because version 1.8.0 is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'core' version 2.5.0 because version 2.6.0-alpha is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.2.0 because version 0.5.0 is already loaded.
  return func(args[0], **pargs)

Out[7]:

	start_time	end_time	duration	mean_zscore	median_zscore	max_zscore	min_zscore	speed_at_start	speed_at_end	max_speed	min_speed	median_speed	mean_speed
id
0	1.625936e+09	1.625936e+09	0.238	1.204139	1.220925	2.258331	0.028349	2.760825	1.517296	3.576624	1.427160	2.851154	2.616020
1	1.625936e+09	1.625936e+09	0.120	1.364368	1.349665	2.412096	0.015503	1.803533	0.497099	1.803533	0.464203	0.553494	0.722099
2	1.625936e+09	1.625936e+09	0.082	1.350428	1.490812	2.229001	0.016666	0.639882	0.830598	0.838116	0.639882	0.791716	0.772154
3	1.625936e+09	1.625936e+09	0.074	1.609420	1.803123	2.578417	0.013637	2.690052	0.684351	2.690052	0.684351	1.327693	1.451886
4	1.625936e+09	1.625936e+09	0.208	1.459232	1.441996	2.610289	0.040791	0.208621	1.136773	1.298535	0.162133	1.088990	0.935486
...	...	...	...	...	...	...	...	...	...	...	...	...	...
160	1.625937e+09	1.625937e+09	0.212	3.099559	3.296528	5.312823	0.013042	1.183369	0.500407	1.183369	0.386452	0.827476	0.791367
161	1.625937e+09	1.625937e+09	0.406	2.234536	2.555549	4.133360	0.013230	0.483370	0.415434	0.967244	0.170981	0.615845	0.603776
162	1.625937e+09	1.625937e+09	0.106	1.272785	1.090846	2.567647	0.029594	1.173970	1.531232	1.586072	1.173970	1.533011	1.472277
163	1.625937e+09	1.625937e+09	0.130	2.206783	2.288842	3.916084	0.000061	1.843658	2.197606	2.263417	1.843658	2.212691	2.156476
164	1.625937e+09	1.625937e+09	0.088	1.682973	1.689252	3.048358	0.021588	1.288769	1.058330	1.334759	1.058330	1.296841	1.260912

165 rows × 13 columns

Plotting¶

From this, we can plot MUA firing rate and speed together.

In [8]:

import matplotlib.pyplot as plt
import numpy as np

fig, axes = plt.subplots(2, 1, sharex=True, figsize=(15, 4))
speed = MuaEventsV1.get_speed(mua_key)  # get speed from MuaEventsV1 table
time = speed.index.to_numpy()
speed = speed.to_numpy()
multiunit_firing_rate = MuaEventsV1.get_firing_rate(
    mua_key, time
)  # get firing rate from MuaEventsV1 table

time_slice = slice(
    np.searchsorted(time, mua_times.loc[10].start_time) - 1_000,
    np.searchsorted(time, mua_times.loc[10].start_time) + 5_000,
)

axes[0].plot(
    time[time_slice],
    multiunit_firing_rate[time_slice],
    color="black",
)
axes[0].set_ylabel("firing rate (Hz)")
axes[0].set_title("multiunit activity")
axes[1].fill_between(time[time_slice], speed[time_slice], color="lightgrey")
axes[1].set_ylabel("speed (cm/s)")
axes[1].set_xlabel("time (s)")

for id, mua_time in mua_times.loc[
    np.logical_and(
        mua_times["start_time"] > time[time_slice].min(),
        mua_times["end_time"] < time[time_slice].max(),
    )
].iterrows():
    axes[0].axvspan(
        mua_time["start_time"], mua_time["end_time"], color="red", alpha=0.5
    )

import matplotlib.pyplot as plt import numpy as np fig, axes = plt.subplots(2, 1, sharex=True, figsize=(15, 4)) speed = MuaEventsV1.get_speed(mua_key) # get speed from MuaEventsV1 table time = speed.index.to_numpy() speed = speed.to_numpy() multiunit_firing_rate = MuaEventsV1.get_firing_rate( mua_key, time ) # get firing rate from MuaEventsV1 table time_slice = slice( np.searchsorted(time, mua_times.loc[10].start_time) - 1_000, np.searchsorted(time, mua_times.loc[10].start_time) + 5_000, ) axes[0].plot( time[time_slice], multiunit_firing_rate[time_slice], color="black", ) axes[0].set_ylabel("firing rate (Hz)") axes[0].set_title("multiunit activity") axes[1].fill_between(time[time_slice], speed[time_slice], color="lightgrey") axes[1].set_ylabel("speed (cm/s)") axes[1].set_xlabel("time (s)") for id, mua_time in mua_times.loc[ np.logical_and( mua_times["start_time"] > time[time_slice].min(), mua_times["end_time"] < time[time_slice].max(), ) ].iterrows(): axes[0].axvspan( mua_time["start_time"], mua_time["end_time"], color="red", alpha=0.5 )

[16:03:49][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False
[16:03:49][WARNING] Spyglass: Multiple classes found in stack: {'`position_v1_trodes_position`.`__trodes_pos_v1`', '`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`position_merge`.`position_output`'}. Please submit a bug report with the snippet used.
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.8.0 is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.5.0 is already loaded.
  return func(args[0], **pargs)
[16:03:50][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.8.0 is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.5.0 is already loaded.
  return func(args[0], **pargs)
[16:03:51][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.8.0 is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.5.0 is already loaded.
  return func(args[0], **pargs)
[16:03:51][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.8.0 is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.5.0 is already loaded.
  return func(args[0], **pargs)
[16:03:52][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.8.0 is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.5.0 is already loaded.
  return func(args[0], **pargs)
[16:03:53][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.8.0 is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.5.0 is already loaded.
  return func(args[0], **pargs)
[16:03:54][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-common' version 1.6.0 because version 1.8.0 is already loaded.
  return func(args[0], **pargs)
/home/dmrodriguez/miniforge3/envs/spyglass/lib/python3.9/site-packages/hdmf/utils.py:668: UserWarning: Ignoring cached namespace 'hdmf-experimental' version 0.3.0 because version 0.5.0 is already loaded.
  return func(args[0], **pargs)

We can also create a figurl to visualize the data.

In [9]:

(MuaEventsV1 & mua_key).create_figurl(
    zscore_mua=True,
)

(MuaEventsV1 & mua_key).create_figurl( zscore_mua=True, )

[16:03:57][WARNING] Spyglass: Upsampled position data, frame indices are invalid. Setting add_frame_ind=False
[16:03:57][WARNING] Spyglass: Multiple classes found in stack: {'`position_v1_trodes_position`.`__trodes_pos_v1`', '`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`position_merge`.`position_output`'}. Please submit a bug report with the snippet used.
[16:03:58][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
[16:03:59][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
[16:04:00][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
[16:04:00][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
[16:04:01][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
[16:04:02][WARNING] Spyglass: Multiple classes found in stack: {'`mua_v1`.`mua_events_parameters`', '`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`__mua_events_v1`', '`spikesorting_v1_curation`.`curation_v1`', '`spikesorting_merge`.`spike_sorting_output`'}. Please submit a bug report with the snippet used.
[16:04:03][WARNING] Spyglass: Multiple classes found in stack: {'`spikesorting_group_v1`.`sorted_spikes_group`', '`mua_v1`.`mua_events_parameters`', '`mua_v1`.`__mua_events_v1`'}. Please submit a bug report with the snippet used.

WARNING: TimeseriesGraph::_add_series y argument is not 1D array. Using squeeze.

Out[9]:

'https://figurl.org/f?v=npm://@fi-sci/figurl-sortingview@12/dist&d=sha1://d1774bae95321e5ace99835c7282ae66c52da796&label=Multiunit%20Detection&zone=franklab.default'

In [ ]: