Accessing Dynamic Routing data

Accessing Dynamic Routing data#

This tutorial walks through the basic contents of a Dynamic Routing session NWB file: the units table, session epochs, trial and performance tables, and the behavioral data (running speed, eye tracking, and keypoint tracking).

Dynamic Routing sessions are stored as NWB files, so the main dependency is PyNWB. Pandas and NumPy are useful for working with the tables and arrays stored in the file.

import pynwb
import pandas as pd
import numpy as np

Loading a session#

Each session is stored as a single NWB file. Pointing pynwb.read_nwb at the file returns an NWBFile object which we can use to explore the file contents.

nwb_path = "/data/ecephys_759434_2025-02-04_12-27-22_nwb_2026-08-04_15-01-21/759434_2025-02-04.nwb.zarr"
nwbfile = pynwb.read_nwb(nwb_path)
nwbfile

/opt/envs/ctlut/lib/python3.10/site-packages/hdmf_zarr/backend.py:1638: UserWarning: Inferred dtype from zarr type. Dataset missing zarr_dtype: data   <zarr.core.Array '/processing/behavior/facemap_front_camera/data' (420648, 500) float32 read-only>
  warnings.warn(
/opt/envs/ctlut/lib/python3.10/site-packages/hdmf_zarr/backend.py:1638: UserWarning: Inferred dtype from zarr type. Dataset missing zarr_dtype: data   <zarr.core.Array '/processing/behavior/facemap_side_camera/data' (420666, 500) float32 read-only>
  warnings.warn(

session_description: ecephys session (day 2) with behavioral task data (day 51) and video recording of behavior

identifier: 819fbc60-9c2a-499c-b185-644d1e8c9eeb

session_start_time

2025-02-04 12:27:22-08:00

timestamps_reference_time

2025-02-04 12:27:22-08:00

file_create_date

0

2026-08-04 21:56:22.390614+00:00

experimenter

('Vayle Lafehr',)

acquisition

frametimes_eye_camera

description: start time of each frame exposure in Eye_20250204T122736

table

	timestamps
id
0	NaN
1	14.42651
2	14.44318
3	14.45984

... and 420651 more row(s).

frametimes_front_camera

description: start time of each frame exposure in Face_20250204T122736

table

	timestamps
id
0	NaN
1	14.64815
2	14.66481
3	14.68148

... and 420644 more row(s).

frametimes_side_camera

description: start time of each frame exposure in Behavior_20250204T122736

table

	timestamps
id
0	NaN
1	14.19090
2	14.20756
3	14.22423

... and 420662 more row(s).

manipulator_positions

description: nominal positions of the motorized stages on each probe's manipulator assembly at the time of ecephys recording

table

	electrode_group_name	device_name	last_movement_time	x	y	z
id
0	probeA	SN40906	-1384	8350.0	6331.0	10257.5
1	probeB	SN40908	-1561	4819.0	13929.5	10251.0
2	probeC	SN40907	-1504	7536.0	9467.0	12441.5
3	probeD	SN41084	-1470	7612.0	4228.0	12097.0

... and 2 more row(s).

keywords

Data type	object
Shape	(17,)
Array size	136.00 bytes

processing

behavior

description: processed behavior data

data_interfaces

facemap_front_camera

resolution: -1.0

comments: no comments

description: motion SVD for video from front camera; shape is number of frames by number of components (500)

conversion: 1.0

offset: 0.0

unit: pixels

data

Data type	float32
Shape	(420648, 500)
Array size	802.32 MiB

timestamps

Data type	float64
Shape	(420648,)
Array size	3.21 MiB

timestamps_unit: seconds

interval: 1

facemap_side_camera

resolution: -1.0

comments: no comments

description: motion SVD for video from side camera; shape is number of frames by number of components (500)

conversion: 1.0

offset: 0.0

unit: pixels

data

Data type	float32
Shape	(420666, 500)
Array size	802.36 MiB

timestamps

Data type	float64
Shape	(420666,)
Array size	3.21 MiB

timestamps_unit: seconds

interval: 1

running_speed

resolution: -1.0

comments: no comments

description: linear forward running speed on a rotating disk, low-pass filtered at 4 Hz with a 3rd order Butterworth filter

conversion: 1.0

offset: 0.0

unit: cm/s

data

Data type	float64
Shape	(412214,)
Array size	3.14 MiB

timestamps

Data type	float64
Shape	(412214,)
Array size	3.14 MiB

timestamps_unit: seconds

interval: 1

dlc_eye_camera

description: DeepLabCut tracking model fit to each frame of eye camera video. Output for every frame includes: `timestamps`: start time of frame exposure, in seconds | `_x` and `_y`: coordinates in pixels, with (0, 0) at top-left of frame | `_likelihood`: likelihood of the model (softmax output of the deep neural network)

table

	cr1_x	cr10_x	cr11_x	cr12_x	cr2_x	cr3_x	cr4_x	cr5_x	cr6_x	cr7_x	cr8_x	cr9_x	eye1_x	eye10_x	eye11_x	eye12_x	eye2_x	eye3_x	eye4_x	eye5_x	eye6_x	eye7_x	eye8_x	eye9_x	pupil1_x	pupil10_x	pupil11_x	pupil12_x	pupil2_x	pupil3_x	pupil4_x	pupil5_x	pupil6_x	pupil7_x	pupil8_x	pupil9_x	cr1_y	cr10_y	cr11_y	cr12_y	cr2_y	cr3_y	cr4_y	cr5_y	cr6_y	cr7_y	cr8_y	cr9_y	eye1_y	eye10_y	eye11_y	eye12_y	eye2_y	eye3_y	eye4_y	eye5_y	eye6_y	eye7_y	eye8_y	eye9_y	pupil1_y	pupil10_y	pupil11_y	pupil12_y	pupil2_y	pupil3_y	pupil4_y	pupil5_y	pupil6_y	pupil7_y	pupil8_y	pupil9_y	cr1_likelihood	cr10_likelihood	cr11_likelihood	cr12_likelihood	cr2_likelihood	cr3_likelihood	cr4_likelihood	cr5_likelihood	cr6_likelihood	cr7_likelihood	cr8_likelihood	cr9_likelihood	eye1_likelihood	eye10_likelihood	eye11_likelihood	eye12_likelihood	eye2_likelihood	eye3_likelihood	eye4_likelihood	eye5_likelihood	eye6_likelihood	eye7_likelihood	eye8_likelihood	eye9_likelihood	pupil1_likelihood	pupil10_likelihood	pupil11_likelihood	pupil12_likelihood	pupil2_likelihood	pupil3_likelihood	pupil4_likelihood	pupil5_likelihood	pupil6_likelihood	pupil7_likelihood	pupil8_likelihood	pupil9_likelihood	timestamps
id
0	6.257579	3.310695	2.865996	61.524036	55.815071	59.706459	61.820957	60.875648	60.541634	63.163883	57.695103	58.799397	-0.263414	4.733630	2.549963	6.088755	4.848226	3.684231	95.296310	4.485808	42.258923	4.645335	51.154285	5.319347	4.342977	62.903099	0.763001	3.143172	2.420771	52.241173	65.632851	62.905418	63.694363	5.825314	5.661117	4.155485	77.114662	155.906342	153.169983	196.260040	199.712463	205.217072	200.374313	197.969772	201.380676	166.143738	191.948074	192.319366	153.580902	154.360458	159.337479	190.358536	156.354660	3.199129	205.206833	87.183762	202.524109	157.757736	196.787369	153.522400	78.079132	190.232651	73.710930	75.290230	78.191711	188.103439	188.820938	192.818100	185.288879	190.196808	182.250031	155.906448	0.001637	0.001441	0.000855	0.001189	0.003616	0.005150	0.020247	0.014635	0.012463	0.009171	0.006167	0.001744	0.004395	0.008654	0.010360	0.001614	0.002157	0.001984	0.004401	0.021181	0.005255	0.043138	0.013506	0.048915	0.005857	0.002141	0.001750	0.004098	0.006094	0.003936	0.007695	0.036590	0.003669	0.002257	0.003137	0.010067	NaN
1	321.738190	313.308655	319.621552	315.709595	313.172668	311.794983	310.274414	305.894470	309.785889	308.276642	308.806885	308.572418	435.308075	299.091217	277.063324	434.011047	416.929474	356.519714	324.248566	352.675964	154.717300	136.778046	171.753586	242.873734	331.124298	267.789185	330.985229	330.398590	327.712616	5.982954	4.909490	4.479672	11.007477	29.517284	269.723846	59.197319	267.661224	258.497620	263.451752	265.682556	268.126038	268.868011	269.503357	269.664581	268.029297	262.367798	261.225098	259.865906	215.143021	123.420181	115.761391	195.713150	357.691925	382.070068	384.816254	381.832977	308.721130	250.920517	171.384689	132.624466	265.426117	124.009918	261.875458	263.757965	266.179779	1.074963	1.035730	6.395949	7.879985	4.490459	208.451828	5.525383	0.038439	0.022409	0.015992	0.029169	0.056433	0.053797	0.062198	0.064636	0.047505	0.030858	0.040817	0.029235	0.575440	0.291975	0.089464	0.119383	0.123169	0.379497	0.317344	0.221876	0.912202	0.690871	0.910316	0.742060	0.004969	0.001009	0.001312	0.003360	0.003718	0.001416	0.001353	0.002571	0.000785	0.000473	0.000631	0.001547	14.42651
2	321.339233	313.104065	313.038055	315.953217	314.643219	313.339600	310.715576	306.432983	310.157776	308.000031	308.471375	307.492188	433.814331	282.424591	291.929199	434.258972	419.676910	371.832520	388.898865	205.979645	153.302017	135.069824	172.569229	242.949860	332.160889	192.276749	331.313538	331.792633	328.397125	6.246439	302.795410	4.368991	303.455597	302.858582	4.636980	303.039062	267.530762	258.950684	260.975342	265.457855	268.325317	268.275940	267.522369	268.252747	268.295837	263.268402	261.609131	260.756714	203.416702	121.928513	116.586853	196.831039	355.412170	373.842804	387.741333	354.879913	309.012512	252.337418	171.487961	133.594513	265.067596	173.010254	260.328369	262.315063	265.579285	2.334807	262.063416	6.798071	263.110260	259.747894	7.379796	233.996796	0.040932	0.050733	0.021523	0.030052	0.056541	0.058877	0.071839	0.106047	0.094316	0.076004	0.082712	0.059780	0.252804	0.241494	0.057785	0.095871	0.156900	0.208213	0.312420	0.634833	0.948794	0.822546	0.855607	0.557850	0.004287	0.001511	0.001133	0.003181	0.004705	0.001977	0.003380	0.003554	0.001372	0.001260	0.000755	0.003432	14.44318
3	320.579498	312.271912	313.338074	316.113678	315.685242	314.214691	313.581909	307.414032	307.389160	307.397705	308.053680	306.923340	433.599457	282.896301	277.046265	429.949493	420.487152	364.821838	389.565002	209.603027	152.213654	136.723816	171.384888	273.462250	331.925690	193.439545	327.908539	331.754486	327.292725	315.606598	302.930267	4.263856	302.485809	302.591370	300.961761	269.504395	269.681976	259.510651	261.928741	266.307831	269.663605	271.359589	271.690430	271.146210	269.531372	267.166412	262.451233	261.354736	203.594498	122.555626	116.950859	197.983719	354.025482	377.177002	388.720428	356.149689	308.834686	251.446457	172.854584	129.080551	265.852722	172.128601	250.567947	262.067993	265.779053	270.581970	262.373962	6.784337	258.818451	259.939362	251.349075	207.556824	0.058540	0.099322	0.053506	0.055305	0.076487	0.090631	0.121970	0.187120	0.200461	0.178605	0.143599	0.125837	0.254278	0.224820	0.070715	0.080775	0.136161	0.100006	0.325625	0.520847	0.944977	0.791974	0.890303	0.469317	0.004967	0.002007	0.001757	0.003880	0.005543	0.003575	0.006451	0.003002	0.002394	0.002453	0.001643	0.005704	14.45984

... and 420651 more row(s).

eye_tracking

description: Ellipses fit to three features in each frame of the eye video: pupil: perimeter of the pupil | eye: inner perimeter of the eyelid | cr: corneal reflection, a bright spot near the center of the eye which is always smaller than the pupil

table

	cr_center_x	cr_center_y	cr_width	cr_height	cr_phi	cr_average_confidence	cr_area	cr_is_bad_frame	eye_center_x	eye_center_y	eye_width	eye_height	eye_phi	eye_average_confidence	eye_area	eye_is_bad_frame	pupil_center_x	pupil_center_y	pupil_width	pupil_height	pupil_phi	pupil_average_confidence	pupil_area	pupil_is_bad_frame	timestamps
id
0	NaN	NaN	NaN	NaN	NaN	0.006526	NaN	True	NaN	NaN	NaN	NaN	NaN	0.013797	NaN	True	NaN	NaN	NaN	NaN	NaN	0.007274	NaN	True	NaN
1	NaN	NaN	NaN	NaN	NaN	0.040957	NaN	True	292.777818	257.166495	154.694249	131.328813	0.152833	0.447800	75179.288538	False	NaN	NaN	NaN	NaN	NaN	0.001929	NaN	True	14.42651
2	NaN	NaN	NaN	NaN	NaN	0.062446	NaN	True	298.465554	259.710655	162.739762	130.362037	0.269021	0.428760	83202.662797	False	NaN	NaN	NaN	NaN	NaN	0.002546	NaN	True	14.44318
3	NaN	NaN	NaN	NaN	NaN	0.115949	NaN	True	301.227109	262.851161	166.508229	131.346907	0.341447	0.400817	87100.625934	False	NaN	NaN	NaN	NaN	NaN	0.003615	NaN	True	14.45984

... and 420651 more row(s).

licks

description: times at which the subject made contact with a combined lick sensor + water spout: putatively the starts of licks, but may include other events such as grooming

table

	timestamps	duration	is_likely_lick
id
0	1533.28359	0.04925	True
1	1533.39764	0.03524	True
2	1534.64212	0.08325	True
3	1534.75918	0.07025	True

... and 2349 more row(s).

lp_front_camera

description: Lightning Pose tracking model fit to 12 facial features for each frame of front camera video. Output for every frame includes: `timestamps`: start time of frame exposure, in seconds | `_x` and `_y`: coordinates in pixels, with (0, 0) at top-left of frame | `_likelihood`: keypoint prediction likelihood between 0 and 1, with higher values representing greater confidence of the model | `_pca_error`: Euclidean distance in pixels between the original keypoint prediction and its prediction after projection to and from PCA space | `_temporal_norm`: Euclidean distance in pixels between keypoint predictions on successive time bins. See original publication for further details: https://doi.org/10.1038/s41592-024-02319-1

table

	ear_base_l_likelihood	ear_base_l_pca_error	ear_base_l_temporal_norm	ear_base_l_x	ear_base_l_y	ear_tip_l_likelihood	ear_tip_l_pca_error	ear_tip_l_temporal_norm	ear_tip_l_x	ear_tip_l_y	eye_bottom_l_likelihood	eye_bottom_l_pca_error	eye_bottom_l_temporal_norm	eye_bottom_l_x	eye_bottom_l_y	eye_top_l_likelihood	eye_top_l_pca_error	eye_top_l_temporal_norm	eye_top_l_x	eye_top_l_y	jaw_likelihood	jaw_pca_error	jaw_temporal_norm	jaw_x	jaw_y	nose_tip_likelihood	nose_tip_pca_error	nose_tip_temporal_norm	nose_tip_x	nose_tip_y	nostril_l_likelihood	nostril_l_pca_error	nostril_l_temporal_norm	nostril_l_x	nostril_l_y	tongue_base_l_likelihood	tongue_base_l_pca_error	tongue_base_l_temporal_norm	tongue_base_l_x	tongue_base_l_y	tongue_tip_likelihood	tongue_tip_pca_error	tongue_tip_temporal_norm	tongue_tip_x	tongue_tip_y	whisker_pad_l_side_likelihood	whisker_pad_l_side_pca_error	whisker_pad_l_side_temporal_norm	whisker_pad_l_side_x	whisker_pad_l_side_y	whisker_pad_l_top_likelihood	whisker_pad_l_top_pca_error	whisker_pad_l_top_temporal_norm	whisker_pad_l_top_x	whisker_pad_l_top_y	timestamps
id
0	0.000136	109.305099	NaN	314.509033	214.964294	0.000172	112.505379	NaN	327.771851	236.113205	0.000122	95.341949	NaN	315.893616	218.793091	0.000139	153.173904	NaN	347.803619	251.166504	0.000169	NaN	NaN	325.692200	243.350540	0.000177	108.735733	NaN	333.152832	244.681915	0.000142	109.330887	NaN	348.895142	256.752350	0.000169	21.836403	NaN	322.884949	247.132492	0.000179	19.428129	NaN	324.289337	246.712814	0.000152	113.855881	NaN	332.498230	243.779175	0.000153	94.381584	NaN	326.739655	240.801239	NaN
1	0.988053	108.866219	112.602974	419.982544	175.533737	0.972307	107.616699	152.396545	450.785309	146.155457	0.994750	102.556816	35.129623	343.112091	196.583969	0.999940	113.204994	76.011208	335.016510	176.238586	0.000171	NaN	0.251405	325.929718	243.432938	0.998823	81.456367	61.697796	273.806396	261.552551	0.993623	66.272217	61.125271	287.769958	256.855408	0.000394	21.391623	5.076637	317.808685	247.194077	0.000154	11.067987	1.821925	326.105865	246.852936	0.996880	107.937508	18.800714	316.760559	233.493622	0.999953	76.962456	27.115084	308.014008	221.190582	14.64815
2	0.994776	108.198898	1.337913	419.241333	176.647568	0.951950	106.964584	1.372030	451.922363	146.923294	0.999444	102.852501	0.658990	342.527039	196.887253	0.999919	113.841293	0.104304	335.117584	176.264343	0.000171	NaN	0.013575	325.942413	243.437744	0.999682	78.570297	3.867516	270.299805	259.921143	0.996092	64.747559	2.752445	285.018280	256.920349	0.000303	21.293278	1.256627	316.664948	247.714630	0.000153	10.681618	1.644859	324.593475	247.499649	0.999597	108.049652	1.690798	315.190399	234.120834	0.998654	77.097771	0.746137	307.282532	221.043396	14.66481
3	0.981099	109.902542	2.212809	421.370148	176.043686	0.971989	108.579208	2.934833	452.630219	144.075104	0.999574	102.235023	0.246029	342.363464	196.703476	0.999908	114.072304	0.302804	335.420380	176.266678	0.000171	NaN	0.042453	325.940369	243.395340	0.998286	81.069862	3.134591	273.171234	261.178345	0.999583	67.042244	2.791916	287.490326	258.217957	0.000386	21.582983	2.758146	314.507233	249.432663	0.000153	11.029763	2.003517	326.456024	246.761414	0.997225	108.192528	1.805767	316.885529	233.498474	0.998660	76.209915	0.386780	307.018433	220.760818	14.68148

... and 420644 more row(s).

lp_side_camera

description: Lightning Pose tracking model fit to 11 facial features for each frame of side camera video. Output for every frame includes: `timestamps`: start time of frame exposure, in seconds | `_x` and `_y`: coordinates in pixels, with (0, 0) at top-left of frame | `_likelihood`: keypoint prediction likelihood between 0 and 1, with higher values representing greater confidence of the model | `_pca_error`: Euclidean distance in pixels between the original keypoint prediction and its prediction after projection to and from PCA space | `_temporal_norm`: Euclidean distance in pixels between keypoint predictions on successive time bins. See original publication for further details: https://doi.org/10.1038/s41592-024-02319-1

table

	ear_base_l_likelihood	ear_base_l_pca_error	ear_base_l_temporal_norm	ear_base_l_x	ear_base_l_y	ear_tip_l_likelihood	ear_tip_l_pca_error	ear_tip_l_temporal_norm	ear_tip_l_x	ear_tip_l_y	eye_bottom_l_likelihood	eye_bottom_l_pca_error	eye_bottom_l_temporal_norm	eye_bottom_l_x	eye_bottom_l_y	eye_top_l_likelihood	eye_top_l_pca_error	eye_top_l_temporal_norm	eye_top_l_x	eye_top_l_y	jaw_likelihood	jaw_pca_error	jaw_temporal_norm	jaw_x	jaw_y	nose_tip_likelihood	nose_tip_pca_error	nose_tip_temporal_norm	nose_tip_x	nose_tip_y	nostril_l_likelihood	nostril_l_pca_error	nostril_l_temporal_norm	nostril_l_x	nostril_l_y	tongue_base_l_likelihood	tongue_base_l_pca_error	tongue_base_l_temporal_norm	tongue_base_l_x	tongue_base_l_y	tongue_tip_likelihood	tongue_tip_pca_error	tongue_tip_temporal_norm	tongue_tip_x	tongue_tip_y	whisker_pad_l_side_likelihood	whisker_pad_l_side_pca_error	whisker_pad_l_side_temporal_norm	whisker_pad_l_side_x	whisker_pad_l_side_y	whisker_pad_l_top_likelihood	whisker_pad_l_top_pca_error	whisker_pad_l_top_temporal_norm	whisker_pad_l_top_x	whisker_pad_l_top_y	timestamps
id
0	0.000168	113.267677	NaN	333.837036	246.252258	0.000165	79.879768	NaN	320.156891	243.217575	0.999803	254.468170	NaN	650.118225	486.369476	0.000017	166.664566	NaN	610.629272	458.189606	0.000160	NaN	NaN	336.275818	242.255692	0.000163	191.183212	NaN	340.532349	239.847870	0.000160	205.411041	NaN	354.644165	239.761612	0.000164	49.634796	NaN	327.532043	241.328751	0.000165	39.109268	NaN	326.956726	241.676346	0.002613	109.493004	NaN	648.755249	153.953262	0.000008	184.805695	NaN	633.057129	423.356537	NaN
1	0.998660	19.148771	140.131393	220.169662	164.297791	0.967683	6.152155	137.327957	225.122482	144.084183	0.998860	21.212503	586.085327	168.429596	152.495071	0.999748	15.346764	544.447571	165.611420	144.530197	0.989995	NaN	182.014877	163.617432	184.649292	0.996758	19.653793	215.132629	136.279358	172.299652	0.999060	13.091238	223.260513	141.179794	174.353531	0.000136	57.599781	23.602236	304.292969	237.204315	0.000078	10.939700	92.018845	238.447937	216.503693	0.999985	44.217010	493.850677	155.161819	169.890945	0.999715	13.460671	547.459656	151.391129	163.145294	14.19090
2	0.998240	16.902878	1.914873	218.254791	164.295212	0.939089	6.250778	0.101881	225.024612	144.055878	0.997475	20.620049	0.258640	168.633972	152.653580	0.999507	13.601815	0.215744	165.710876	144.721649	0.993864	NaN	0.637287	163.055664	184.950211	0.996525	18.983356	0.148255	136.160416	172.211151	0.998986	12.116210	0.101311	141.197617	174.253799	0.000125	49.693466	16.330482	289.068665	231.296249	0.000076	7.766047	5.381122	233.339066	214.813751	0.999973	40.651848	0.202028	155.162720	170.092972	0.999431	11.975651	0.162747	151.438599	163.300964	14.20756
3	0.999538	19.867174	1.068522	217.237686	163.967743	0.991282	10.473170	1.310066	224.011932	143.224762	0.999953	26.064354	0.535453	168.833847	153.150330	0.998141	16.130512	0.469745	165.988861	145.100311	0.985022	NaN	0.577968	163.633423	184.934647	0.997510	24.649723	0.114425	136.125870	172.102066	0.999287	15.488349	0.151104	141.086517	174.151382	0.000143	49.942989	20.518162	308.121674	238.910568	0.000130	14.331257	52.997490	283.749512	231.169815	0.999961	52.588783	0.259248	155.409256	170.173157	0.999686	13.902470	0.186598	151.563370	163.439713	14.22423

... and 420662 more row(s).

quiescent_interval_violations

description: times at which the subject made contact with the lick spout during a pre-trial quiescent interval, triggering a restart of the trial

table

	timestamps
id
0	2600.32356
1	2602.02498
2	2785.17845
3	2797.55546

... and 25 more row(s).

rewards

description: water rewards delivered to the subject

table

	timestamps	duration	is_solenoid_time
id
0	1632.19683	0.04145	True
1	1722.70581	0.05076	True
2	1813.21498	0.04144	True
3	1903.72414	0.04141	True

... and 152 more row(s).

ecephys

description: processed ecephys data

electrodes

description: metadata about extracellular electrodes

table

	location	group	group_name	structure	x	y	z	channel	rel_x	rel_y	reference	imp	raw_structure
id
0	CP	probeB pynwb.ecephys.ElectrodeGroup at 0x140171177370256\nFields:\n description: Neuropixels 1.0\n device: 17131307152 pynwb.device.Device at 0x140171179058336\nFields:\n description: Neuropixels 1.0\n manufacturer: imec\n\n location: 2011 B4\n	probeB	CP	4625.0	5100.0	2900.0	0	27	0	tip	150000.0	CP
1	CP	probeB pynwb.ecephys.ElectrodeGroup at 0x140171177370256\nFields:\n description: Neuropixels 1.0\n device: 17131307152 pynwb.device.Device at 0x140171179058336\nFields:\n description: Neuropixels 1.0\n manufacturer: imec\n\n location: 2011 B4\n	probeB	CP	4625.0	5075.0	2900.0	1	59	0	tip	150000.0	CP
2	CP	probeB pynwb.ecephys.ElectrodeGroup at 0x140171177370256\nFields:\n description: Neuropixels 1.0\n device: 17131307152 pynwb.device.Device at 0x140171179058336\nFields:\n description: Neuropixels 1.0\n manufacturer: imec\n\n location: 2011 B4\n	probeB	CP	4625.0	5075.0	2900.0	2	11	20	tip	150000.0	CP
3	CP	probeB pynwb.ecephys.ElectrodeGroup at 0x140171177370256\nFields:\n description: Neuropixels 1.0\n device: 17131307152 pynwb.device.Device at 0x140171179058336\nFields:\n description: Neuropixels 1.0\n manufacturer: imec\n\n location: 2011 B4\n	probeB	CP	4625.0	5075.0	2900.0	3	43	20	tip	150000.0	CP

... and 1916 more row(s).

electrode_groups

probeB

description: Neuropixels 1.0

location: 2011 B4

device

description: Neuropixels 1.0

manufacturer: imec

probeC

description: Neuropixels 1.0

location: 2011 E2

device

description: Neuropixels 1.0

manufacturer: imec

probeD

description: Neuropixels 1.0

location: 2011 D1

device

description: Neuropixels 1.0

manufacturer: imec

probeE

description: Neuropixels 1.0

location: 2011 A3

device

description: Neuropixels 1.0

manufacturer: imec

probeF

description: Neuropixels 1.0

location: 2011 A1

device

description: Neuropixels 1.0

manufacturer: imec

devices

17131307152

description: Neuropixels 1.0

manufacturer: imec

17216703422

description: Neuropixels 1.0

manufacturer: imec

18005120322

description: Neuropixels 1.0

manufacturer: imec

20097906862

description: Neuropixels 1.0

manufacturer: imec

22175718152

description: Neuropixels 1.0

manufacturer: imec

SN40902

description: motorized 3-axis micromanipulator for positioning and inserting probeF

manufacturer: NewScale

SN40903

description: motorized 3-axis micromanipulator for positioning and inserting probeE

manufacturer: NewScale

SN40907

description: motorized 3-axis micromanipulator for positioning and inserting probeC

manufacturer: NewScale

SN40908

description: motorized 3-axis micromanipulator for positioning and inserting probeB

manufacturer: NewScale

SN41084

description: motorized 3-axis micromanipulator for positioning and inserting probeD

manufacturer: NewScale

intervals

aud_rf_mapping_trials

description: auditory receptive-field mapping trials

table

	start_time	stop_time	stim_start_time	stim_stop_time	trial_index	is_AM_noise	is_white_noise	is_pure_tone	freq
id
0	47.16778	47.66817	47.17536	47.42536	3	False	False	True	13000.0
1	48.75244	49.25278	48.76060	49.01060	6	True	False	False	0.0
2	49.30286	49.80327	49.31036	49.56036	7	False	False	True	10000.0
3	51.40474	51.90502	51.41254	51.66254	11	False	False	True	12000.0

... and 428 more row(s).

epochs

description: time intervals corresponding to different phases of the session; each epoch corresponds to one TaskControl subclass that controlled stimulus presentation during the epoch, which corresponds to one .hdf5 stimulus file

table

	start_time	stop_time	script_name	interval_names	tags
id
0	45.62740	916.491240	RFMapping	[vis_rf_mapping_trials, aud_rf_mapping_trials]	[mapping]
1	927.69937	1530.872170	Spontaneous	[]	[spontaneous]
2	1541.98091	2145.086620	SpontaneousRewards	[]	[rewards, spontaneous]
3	2155.69515	5796.812075	DynamicRouting1	[trials, performance]	[task, rewards]

... and 2 more row(s).

performance

description: behavioral performance for each context block in task (refers to `trials` or `intervals['DynamicRouting1'])

table

	start_time	stop_time	block_index	n_trials	n_responses	n_hits	n_contingent_rewards	hit_rate	false_alarm_rate	catch_response_rate	rewarded_modality	is_first_block_aud	cross_modality_dprime	signed_cross_modality_dprime	vis_dprime	aud_dprime	vis_target_response_rate	vis_nontarget_response_rate	aud_target_response_rate	aud_nontarget_response_rate
id
0	2158.88748	2763.96067	0	92	25.0	24.0	24.0	1.000000	0.016667	3.125000	vis	False	3.681688	3.681688	3.996798	0.000000	1.000000	0.00	0.05	0.000000
1	2764.91140	3369.10091	1	89	38.0	21.0	21.0	0.954545	0.280702	3.800000	aud	False	1.889823	-1.889823	0.000000	1.889823	0.421053	0.00	1.00	0.421053
2	3369.86822	3976.22623	2	89	26.0	24.0	24.0	0.960000	0.035088	3.714286	vis	False	3.688618	3.688618	3.395540	-0.344713	1.000000	0.05	0.00	0.055556
3	3976.52642	4584.60250	3	89	36.0	23.0	23.0	1.000000	0.228070	4.000000	aud	False	2.498592	-2.498592	-0.293078	2.449813	0.315789	0.05	1.00	0.333333

... and 2 more row(s).

trials

description: visual-auditory task-switching behavior trials

table

	start_time	stop_time	quiescent_start_time	quiescent_stop_time	stim_start_time	stim_stop_time	response_window_start_time	response_window_stop_time	task_control_response_time	response_time	reward_time	post_response_window_start_time	post_response_window_stop_time	stim_name	grating_phase	block_index	rewarded_modality	trial_index	trial_index_in_block	repeat_index	is_response	is_correct	is_incorrect	is_hit	is_false_alarm	is_correct_reject	is_miss	is_go	is_nogo	is_rewarded	is_noncontingent_reward	is_contingent_reward	is_reward_scheduled	is_instruction	is_aud_stim	is_vis_stim	is_catch	is_target	is_aud_target	is_vis_target	is_nontarget	is_aud_nontarget	is_vis_nontarget	is_vis_rewarded	is_aud_rewarded	is_block_switch	is_repeat	is_opto	is_task_control_correct
id
0	2158.88748	2164.39167	2158.88748	2160.35497	2160.415740	2160.916160	2160.47170	2161.38916	2161.07221	2161.06612	2161.08891	2161.416585	2164.419100	vis1	0.0	0	vis	0	0.0	0.0	True	True	False	True	False	False	False	True	False	True	False	True	True	True	False	True	False	True	False	True	False	False	False	True	False	False	False	False	False
1	2165.30909	2170.81367	2165.30909	2166.77695	2166.837800	2167.338220	2166.89376	2167.81124	2167.22735	2167.21475	2167.24403	2167.838630	2170.841150	vis1	0.0	0	vis	1	1.0	0.0	True	True	False	True	False	False	False	True	False	True	False	True	True	True	False	True	False	True	False	True	False	False	False	True	False	False	False	False	False
2	2172.76534	2178.28664	2172.76534	2174.23327	2174.294050	2174.794460	2174.34997	2175.26747	2174.60025	2174.59576	2174.61690	2175.294885	2178.314305	vis1	0.0	0	vis	2	2.0	0.0	True	True	False	True	False	False	False	True	False	True	False	True	True	True	False	True	False	True	False	True	False	False	False	True	False	False	False	False	False
3	2179.65444	2185.17571	2179.65444	2181.12234	2181.183375	2181.683795	2181.23910	2182.15653	2181.47267	2181.46901	2181.48934	2182.184205	2185.203190	vis1	0.5	0	vis	3	3.0	0.0	True	True	False	True	False	False	False	True	False	True	False	True	True	True	False	True	False	True	False	True	False	False	False	True	False	False	False	False	False

... and 541 more row(s).

vis_rf_mapping_trials

description: visual receptive-field mapping trials

table

	start_time	stop_time	stim_start_time	stim_stop_time	trial_index	is_small_field_grating	grating_orientation	grating_x	grating_y	is_full_field_flash	flash_contrast
id
0	45.59974	46.10021	45.62740	45.877560	0	True	90.0	-798.722753	-146.240918	False	NaN
1	46.11685	46.61727	46.14445	46.394670	1	True	225.0	159.744551	438.722753	False	NaN
2	46.63393	47.13435	46.66157	46.911785	2	True	270.0	798.722753	438.722753	False	NaN
3	47.68485	48.18523	47.71243	47.962640	4	True	90.0	159.744551	438.722753	False	NaN

... and 1220 more row(s).

subject

age: P177D

age__reference: birth

genotype: VGAT-ChR2-YFP/wt

sex: M

species: Mus musculus

subject_id: 759434

date_of_birth

2024-08-11 00:00:00-07:00

strain: VGAT-ChR2-YFP(ND)

epochs

description: time intervals corresponding to different phases of the session; each epoch corresponds to one TaskControl subclass that controlled stimulus presentation during the epoch, which corresponds to one .hdf5 stimulus file

table

	start_time	stop_time	script_name	interval_names	tags
id
0	45.62740	916.491240	RFMapping	[vis_rf_mapping_trials, aud_rf_mapping_trials]	[mapping]
1	927.69937	1530.872170	Spontaneous	[]	[spontaneous]
2	1541.98091	2145.086620	SpontaneousRewards	[]	[rewards, spontaneous]
3	2155.69515	5796.812075	DynamicRouting1	[trials, performance]	[task, rewards]

... and 2 more row(s).

trials

description: visual-auditory task-switching behavior trials

table

	start_time	stop_time	quiescent_start_time	quiescent_stop_time	stim_start_time	stim_stop_time	response_window_start_time	response_window_stop_time	task_control_response_time	response_time	reward_time	post_response_window_start_time	post_response_window_stop_time	stim_name	grating_phase	block_index	rewarded_modality	trial_index	trial_index_in_block	repeat_index	is_response	is_correct	is_incorrect	is_hit	is_false_alarm	is_correct_reject	is_miss	is_go	is_nogo	is_rewarded	is_noncontingent_reward	is_contingent_reward	is_reward_scheduled	is_instruction	is_aud_stim	is_vis_stim	is_catch	is_target	is_aud_target	is_vis_target	is_nontarget	is_aud_nontarget	is_vis_nontarget	is_vis_rewarded	is_aud_rewarded	is_block_switch	is_repeat	is_opto	is_task_control_correct
id
0	2158.88748	2164.39167	2158.88748	2160.35497	2160.415740	2160.916160	2160.47170	2161.38916	2161.07221	2161.06612	2161.08891	2161.416585	2164.419100	vis1	0.0	0	vis	0	0.0	0.0	True	True	False	True	False	False	False	True	False	True	False	True	True	True	False	True	False	True	False	True	False	False	False	True	False	False	False	False	False
1	2165.30909	2170.81367	2165.30909	2166.77695	2166.837800	2167.338220	2166.89376	2167.81124	2167.22735	2167.21475	2167.24403	2167.838630	2170.841150	vis1	0.0	0	vis	1	1.0	0.0	True	True	False	True	False	False	False	True	False	True	False	True	True	True	False	True	False	True	False	True	False	False	False	True	False	False	False	False	False
2	2172.76534	2178.28664	2172.76534	2174.23327	2174.294050	2174.794460	2174.34997	2175.26747	2174.60025	2174.59576	2174.61690	2175.294885	2178.314305	vis1	0.0	0	vis	2	2.0	0.0	True	True	False	True	False	False	False	True	False	True	False	True	True	True	False	True	False	True	False	True	False	False	False	True	False	False	False	False	False
3	2179.65444	2185.17571	2179.65444	2181.12234	2181.183375	2181.683795	2181.23910	2182.15653	2181.47267	2181.46901	2181.48934	2182.184205	2185.203190	vis1	0.5	0	vis	3	3.0	0.0	True	True	False	True	False	False	False	True	False	True	False	True	True	True	False	True	False	True	False	True	False	False	False	True	False	False	False	False	False

... and 541 more row(s).

units

description: spike-sorted units from Kilosort 2.5

waveform_unit: volts

table

	activity_drift	amplitude	amplitude_cutoff	amplitude_cv_median	amplitude_cv_range	amplitude_median	ccf_ap	ccf_dv	ccf_ml	cluster_id	d_prime	decoder_label	decoder_probability	default_qc	device_name	drift_mad	drift_ptp	drift_std	electrode_group_name	exp_decay	firing_range	firing_rate	half_width	is_not_drift	is_qc_pass	isi_violations_count	isi_violations_ratio	isolation_distance	l_ratio	location	nn_hit_rate	nn_miss_rate	num_negative_peaks	num_positive_peaks	num_spikes	peak_channel	peak_electrode	peak_to_valley	peak_trough_ratio	presence_ratio	recovery_slope	repolarization_slope	rp_contamination	rp_violations	silhouette	sliding_rp_violation	snr	spike_amplitudes	spread	structure	sync_spike_2	sync_spike_4	sync_spike_8	unit_id	velocity_above	velocity_below	spike_times	obs_intervals	electrode_group
id
0	0.310182	86.687622	0.002210	0.292047	0.291903	67.860000	4625.0	5100.0	2900.0	0	3.193662	sua	0.610000	False	17131307152	NaN	NaN	NaN	probeB	0.016415	4.20	1.471540	0.000230	False	False	6.0	0.131851	80.178739	0.232173	CP	0.723523	0.010892	1	1	10308.0	0	0	0.000833	-0.305959	1.000000	-36971.794863	202197.022806	0.141922	4.0	0.113555	0.205	3.821928	[-56.159996, -60.839996, -74.88, -44.46, -21.06, -86.579994, -112.31999, -58.499996, -25.74, -67.86, -67.86, -67.86, -77.21999, -44.46, -65.52, -39.78, -86.579994, -79.56, -86.579994, -46.8, -23.4, -88.92, -98.28, -58.499996, -67.86, -65.52, -46.8, -72.54, -65.52, -74.88, -42.12, -70.2, -63.179996, -35.1, -46.8, -74.88, -53.82, -39.78, -42.12, -72.54, -84.24, -86.579994, -35.1, -77.21999, -56.159996, -84.24, -63.179996, -67.86, -42.12, -56.159996, -56.159996, -53.82, -11.7, -81.899994, -35.1, -28.079998, -65.52, -84.24, -70.2, -79.56, -46.8, -44.46, -93.6, -63.179996, -70.2, -30.419998, -56.159996, -88.92, -60.839996, -58.499996, -53.82, -93.6, -67.86, -56.159996, -79.56, -86.579994, -53.82, -65.52, -37.44, -67.86, -37.44, -74.88, -88.92, -63.179996, -102.96, -53.82, -58.499996, -67.86, -74.88, -79.56, -81.899994, -46.8, -51.48, -77.21999, -58.499996, -51.48, -42.12, -70.2, -74.88, -77.21999, ...]	80.0	CP	0.034051	0.000097	0.0	759434_2025-02-04_B-0	301.814836	NaN	[20.899214575483686, 21.360979519709296, 22.053843601906184, 22.133443304989328, 22.723007772506712, 22.799074155436248, 23.10067303043468, 23.64303767401332, 25.113465522466676, 25.205898511013388, 25.372797888457814, 25.697596676917666, 25.769329742677684, 25.904195906276673, 26.236827998850654, 26.490660385357405, 26.526160252938453, 26.644159812785322, 26.84085907907243, 26.956058649363612, 27.07945818906788, 27.092058142068474, 27.336390564011282, 27.622722829289415, 27.7567556626635, 27.784922224265365, 27.837022029926565, 27.927588358769487, 28.126187617969386, 28.513219507625312, 28.825251677039585, 29.15318378714509, 29.366282992258373, 31.292175808437037, 31.30347576628678, 32.33060526829847, 32.88486986748878, 33.07016917629916, 34.4509306925525, 34.57699688897647, 35.1373947986221, 35.15066141580262, 35.56365987526666, 35.944525121258266, 36.06372467662901, 36.08882458300321, 36.15569100024977, 37.462486125740334, 38.546815414389656, 39.16374644649299, 39.25457944100789, 39.62457806086671, 40.70814068570912, 40.71050734354786, 40.773007110415904, 40.93457317442092, 41.19720552810269, 43.2934310422524, 44.00382839238134, 44.1568611548833, 44.17692774669907, 45.18009067144243, 45.584922494702376, 46.138387096876784, 46.42835268193551, 48.10991307617137, 48.24014592371987, 49.26114211527624, 50.25200508589997, 50.507270800393556, 51.93676546819947, 52.3111307384368, 52.782662312898324, 52.81066220845521, 53.25756054146848, 53.454859805517515, 53.70432554164575, 53.88459153589769, 54.145823894801616, 54.312256607320094, 54.33275653085281, 54.44188945710667, 54.62105545546173, 54.738921682472615, 54.97258747753661, 55.08525372394407, 55.13465353967657, 55.38005262430726, 55.76781784456111, 55.98335037393112, 56.463948581239634, 56.47734853125614, 56.49241514172246, 56.653947872518486, 57.14964602350232, 57.36174523234571, 57.40441173986097, 57.64621083792006, 57.74407713953316, 57.77134370449213, ...]	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x140171177370256\nFields:\n description: Neuropixels 1.0\n device: 17131307152 pynwb.device.Device at 0x140171179058336\nFields:\n description: Neuropixels 1.0\n manufacturer: imec\n\n location: 2011 B4\n
1	0.175051	251.456230	0.000043	NaN	NaN	124.020000	4625.0	5100.0	2900.0	1	8.154771	sua	0.700000	False	17131307152	NaN	NaN	NaN	probeB	0.039808	3.60	1.129637	0.000157	False	False	0.0	0.000000	128.928950	0.000242	CP	0.955407	0.000584	1	1	7913.0	0	0	0.000737	-0.261612	0.974138	-62186.686358	586372.319335	0.000000	0.0	0.253279	0.040	5.911899	[-119.34, -152.09999, -112.31999, -133.37999, -102.96, -119.34, -95.939995, -119.34, -126.35999, -119.34, -121.67999, -88.92, -98.28, -126.35999, -128.7, -107.64, -161.45999, -109.979996, -91.259995, -107.64, -93.6, -128.7, -135.72, -128.7, -112.31999, -109.979996, -98.28, -138.06, -128.7, -128.7, -112.31999, -105.299995, -119.34, -119.34, -95.939995, -91.259995, -105.299995, -114.659996, -147.42, -91.259995, -138.06, -128.7, -131.04, -93.6, -102.96, -70.2, -142.73999, -116.99999, -121.67999, -142.73999, -107.64, -100.619995, -119.34, -133.37999, -109.979996, -100.619995, -102.96, -156.78, -133.37999, -140.4, -116.99999, -109.979996, -95.939995, -152.09999, -116.99999, -112.31999, -112.31999, -105.299995, -116.99999, -98.28, -126.35999, -112.31999, -138.06, -109.979996, -121.67999, -95.939995, -119.34, -138.06, -119.34, -145.08, -107.64, -98.28, -131.04, -102.96, -116.99999, -109.979996, -107.64, -100.619995, -114.659996, -79.56, -116.99999, -102.96, -114.659996, -114.659996, -107.64, -119.34, -114.659996, -100.619995, -140.4, -116.99999, ...]	40.0	CP	0.040819	0.000000	0.0	759434_2025-02-04_B-1	NaN	NaN	[20.57621578030963, 20.593715715032687, 20.804348262680243, 21.13564702689437, 21.19894679077833, 21.28967978566623, 21.415279317164252, 21.622611877121177, 21.703744907818148, 21.88721089013373, 22.104076747863594, 22.116776700491183, 22.41647558257683, 22.59794157235263, 22.802440809544873, 23.01360668853637, 23.45797169766592, 24.795766707523033, 25.067999025395736, 25.13579877249419, 25.239231720009677, 25.278631573043292, 25.288531536115194, 25.445897615786677, 25.599663708886567, 25.786696344564753, 25.949462404093637, 26.037495409052838, 26.235728002953778, 26.4062273669698, 26.815292507772277, 26.906692166840106, 28.21005397180405, 28.379020008206247, 28.533052766978102, 28.630985735009205, 28.744651977686555, 28.833251647198693, 29.083284047879868, 29.099650653497047, 29.279783314912997, 29.3920828960215, 29.759114860279652, 29.955080795968847, 30.068547039392215, 30.288679551603717, 30.510078725757076, 31.35727556560679, 31.79400726987619, 32.07477288925194, 32.146372622175974, 32.306772023866124, 32.39303836874852, 32.434438214321915, 32.504404620005126, 32.62020418805824, 32.77583694086192, 32.96053625191036, 33.175202117846474, 33.87843282804121, 33.97566579868339, 34.103465321975165, 34.26789804195386, 34.925528922241675, 35.21619450468933, 35.25499435996101, 35.784425718449086, 36.93868807957263, 37.16508723507543, 37.29692007665576, 37.62208553041457, 38.14281692135462, 38.36238276901318, 38.52451549757114, 38.64928169884425, 38.709914806008506, 38.766114596376255, 38.93048064993695, 39.03944691014583, 39.203046299899626, 39.597744827624695, 39.83141062268869, 40.1116762439295, 40.25964235866404, 40.3695419487248, 40.46520825854415, 40.52070805152298, 40.766107136153664, 40.776107098852556, 40.78540706416252, 40.835340211238965, 40.88767334936314, 41.05900604360407, 41.132239103768924, 41.272771912897284, 41.29243850620509, 41.30933844316621, 42.241168300657506, 42.6940999444991, 43.15633155365066, ...]	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x140171177370256\nFields:\n description: Neuropixels 1.0\n device: 17131307152 pynwb.device.Device at 0x140171179058336\nFields:\n description: Neuropixels 1.0\n manufacturer: imec\n\n location: 2011 B4\n
2	0.054430	98.420357	0.000126	0.274439	0.277458	72.540000	4675.0	5050.0	2900.0	2	3.409922	sua	0.580000	True	17131307152	3.930478	23.582832	2.881839	probeB	0.026793	6.20	3.153219	0.000203	True	True	31.0	0.148364	85.431802	0.395914	CP	0.606742	0.006987	1	1	22088.0	5	5	0.000607	-0.294815	1.000000	-38930.572298	326048.211633	0.190425	24.0	0.111605	0.180	4.371770	[-49.14, -37.44, -9.36, -30.419998, -51.48, -37.44, -16.38, -28.079998, -49.14, -58.499996, -65.52, 4.68, -44.46, -25.74, -37.44, -39.78, -46.8, -39.78, -51.48, -56.159996, -44.46, -25.74, -21.06, -37.44, -39.78, -60.839996, -63.179996, -49.14, -81.899994, -32.76, -46.8, -23.4, -60.839996, -37.44, -49.14, -30.419998, -30.419998, -53.82, -49.14, -9.36, -37.44, -25.74, -16.38, -77.21999, -53.82, -35.1, -49.14, -25.74, -42.12, -51.48, -32.76, -30.419998, -70.2, -25.74, -44.46, -49.14, -49.14, -60.839996, -60.839996, -16.38, -60.839996, -56.159996, -60.839996, -70.2, -53.82, -60.839996, -53.82, -44.46, -28.079998, -72.54, -65.52, -42.12, -16.38, -53.82, -53.82, -58.499996, -51.48, -63.179996, -37.44, -37.44, -32.76, -35.1, -49.14, -49.14, -63.179996, -53.82, -37.44, -42.12, -51.48, -44.46, -51.48, -56.159996, -11.7, -37.44, -21.06, -79.56, -49.14, -11.7, -37.44, -51.48, ...]	80.0	CP	0.038799	0.000000	0.0	759434_2025-02-04_B-2	NaN	NaN	[20.31891674006727, 20.34118332367679, 20.5163160037433, 20.88228130531357, 20.889014613530822, 20.91058119975142, 20.96881431586794, 21.10764713133749, 21.256646575550906, 21.355246207761933, 21.38574609399354, 21.414179321267376, 21.51224562213446, 21.931044059963853, 22.135976628873046, 22.226742956969943, 22.304376000722304, 22.360342458627073, 22.46820872293907, 22.58224163091538, 22.622374814546912, 23.165272789469494, 23.307638925092647, 24.027669572621516, 25.29089819395393, 26.31269438252621, 26.44289389686572, 26.49232704580722, 26.539893535044925, 26.611426601550967, 26.685926323657675, 26.69835961061329, 26.846725723855776, 26.878392272402255, 26.89929219444293, 26.919125453795722, 26.95182533182108, 27.07662486630319, 27.38035706667739, 27.43769018615101, 27.502856609738757, 27.735689074577845, 27.88642184565907, 28.405719908612276, 28.564452649852612, 28.586052569282206, 28.627852413363556, 28.700752141438443, 28.82888499682018, 28.935317933145335, 29.049017509031682, 29.070717428088265, 29.13851717518672, 29.36971631278499, 29.544615660388526, 29.63578198699338, 29.777681457690587, 30.15018006822413, 31.03567676521058, 31.15744297767403, 31.184542876588015, 31.363242210017127, 31.651807800298013, 32.11500607251046, 32.31493866007021, 32.84303669019844, 32.91400309215154, 33.09893573566296, 33.27936839595988, 33.38696799459991, 33.40020127857143, 33.94349925200197, 34.45139735747844, 34.59133016884487, 34.5982634763161, 35.01909523989426, 35.17186133672426, 35.51842671065869, 35.523760024098095, 35.575359831624354, 35.775092419930125, 35.87832536819164, 36.09992454159897, 36.547456205583174, 37.471819424259294, 37.576885699015605, 37.67681865958648, 38.22998326287992, 38.395249313083525, 38.40464927802048, 38.437682488135806, 38.46354905831693, 38.49548227253537, 38.531548804669356, 38.65271501937087, 38.67684826268419, 38.7549479713625, 38.76731459190012, 38.78491452625016, 38.81398108449493, ...]	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x140171177370256\nFields:\n description: Neuropixels 1.0\n device: 17131307152 pynwb.device.Device at 0x140171179058336\nFields:\n description: Neuropixels 1.0\n manufacturer: imec\n\n location: 2011 B4\n
3	0.053826	65.543402	0.000125	NaN	NaN	30.419998	4625.0	5075.0	2900.0	3	2.121909	noise	0.709971	False	17131307152	0.000000	0.000000	0.000000	probeB	0.001586	15.61	3.113104	0.000293	True	False	1282.0	6.294732	40.654845	3.545498	CP	0.337900	0.024771	2	2	21807.0	2	2	0.000420	-0.333450	1.000000	-13325.179709	128286.029172	1.000000	514.0	0.002879	NaN	2.235933	[-16.38, -23.4, -14.039999, -39.78, -18.72, -58.499996, -28.079998, -51.48, -84.24, -4.68, -95.939995, -23.4, -39.78, -11.7, -44.46, -9.36, -23.4, -49.14, -9.36, -21.06, -46.8, -21.06, -35.1, -39.78, -18.72, -9.36, -30.419998, -25.74, -2.34, 9.36, -16.38, -16.38, -23.4, -16.38, -37.44, -9.36, -42.12, -14.039999, -21.06, -25.74, -18.72, -11.7, -51.48, -58.499996, -67.86, -25.74, -18.72, -37.44, -60.839996, -25.74, -28.079998, 4.68, -58.499996, -9.36, -11.7, -28.079998, -25.74, 2.34, -32.76, -72.54, -28.079998, -21.06, -16.38, -53.82, -49.14, -9.36, -39.78, -39.78, -49.14, -18.72, -53.82, -39.78, -32.76, -11.7, -21.06, -53.82, -51.48, -60.839996, -23.4, -39.78, -63.179996, -25.74, -46.8, -23.4, 2.34, -35.1, -18.72, -18.72, -11.7, -21.06, -2.34, 11.7, -7.0199995, -49.14, -46.8, -23.4, -72.54, -32.76, -30.419998, -35.1, ...]	80.0	CP	0.175586	0.000596	0.0	759434_2025-02-04_B-3	NaN	NaN	[33.335501519909634, 33.34220149491789, 33.34380148894971, 33.348434805000196, 33.35783476993715, 33.4804676458345, 33.49443426040394, 33.498300912647515, 33.506267549597624, 33.5244674817096, 34.00896567447068, 34.017932307690685, 37.32041998899814, 46.71121829347803, 46.87921766681933, 46.884250981377775, 46.900617586994954, 49.32117522467856, 49.36504172771768, 49.54120773726308, 50.0100059885869, 50.02453926770929, 50.14807214024954, 50.38367126143531, 50.38663791703598, 59.353937801218, 59.499837256994766, 59.50707056334696, 59.52413716635306, 59.529070481284506, 65.04848322651725, 65.12138295459214, 68.02020547495451, 68.14827166391827, 68.16227161169671, 68.18677152030898, 68.18967150949166, 68.29307112379814, 68.30640440739667, 68.31207105292603, 68.32413767458269, 68.32527100368857, 69.23836759772394, 69.2416009189966, 71.71295836719054, 72.16239002408753, 72.18955658941951, 80.08552713646074, 80.09232711109598, 80.10009374879212, 80.12559365367429, 80.14066026414062, 80.15309355109622, 80.16396017722903, 80.1738934735099, 80.17512680224277, 80.20842667803007, 80.21792664259402, 80.88545748595372, 80.88969080349625, 80.89402412066576, 81.0438235618951, 81.06995679774819, 81.08449007687057, 81.09432337352447, 88.30962979286147, 88.31959642235137, 88.32459640370081, 88.33189637647101, 88.33726302311939, 99.81355354845218, 99.82815349399257, 99.84528676341665, 103.02114158374721, 103.02914155390633, 110.0082488542956, 110.04354872262269, 111.38241039516768, 111.39247702428455, 111.40354364967132, 111.52500986325381, 118.2821179917278, 118.67251653549235, 118.67804984818574, 118.79678273863053, 118.80084939012806, 118.8076826979723, 118.80881602707817, 118.84398256256927, 118.97971538960215, 118.99048201610796, 118.9919820105128, 119.01108193926765, 124.38542855894855, 124.38906187872914, 124.42219508847145, 142.68932694978247, 142.70746021547646, 142.8696262772434, 142.88639288136855, ...]	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x140171177370256\nFields:\n description: Neuropixels 1.0\n device: 17131307152 pynwb.device.Device at 0x140171179058336\nFields:\n description: Neuropixels 1.0\n manufacturer: imec\n\n location: 2011 B4\n

... and 2281 more row(s).

experiment_description: visual-auditory task-switching behavior experiment

session_id: 759434_2025-02-04

lab: NP3

institution: Neural Circuits & Behavior | MindScope program | Allen Institute for Neural Dynamics

source_script: https://raw.githubusercontent.com/samgale/DynamicRoutingTask/9cabb82b8284f6b15f9b37ac8179141bb1102548/DynamicRouting1.py

source_script_file_name: https://github.com/AllenInstitute/npc_sessions/releases/tag/v0.0.289

stimulus_notes: stage 5 ori AMN moving

Units#

The “units” from an electrophysiological recording are the outputs of a clustering algorithm (in this case, Kilosort), which assigns each spike detected in the voltage traces to a unique neuron. The units table has one row per unit and contains spike times, waveforms, quality-control metrics, and anatomical location for every sorted unit in the session.

Column	Description
activity_drift	Measure of drift in unit activity over the session
amplitude	Amplitude (µV) of the average spike waveform
amplitude_cutoff	Estimated fraction of spikes missing from this unit (default threshold = 0.1)
amplitude_cv_median	Median coefficient of variation of spike amplitudes
amplitude_cv_range	Range of coefficient of variation of spike amplitudes
amplitude_median	Median spike amplitude (µV)
ccf_ap	Anterior-posterior coordinate in Allen CCF atlas (µm)
ccf_dv	Dorsal-ventral coordinate in Allen CCF atlas (µm)
ccf_ml	Medial-lateral coordinate in Allen CCF atlas (µm)
cluster_id	Identifier for this unit assigned by the spike sorting algorithm (unique within each probe)
d_prime	Measure of how separable this unit’s waveforms are from its neighbors’
decoder_label	Predicted cell type label from decoder
decoder_probability	Confidence of decoder cell type prediction [0-1]
default_qc	Whether the unit passes default quality control criteria
device_name	Name of the recording device
drift_mad	Median absolute deviation of unit drift
drift_ptp	Peak-to-peak amplitude of unit drift (µm)
drift_std	Standard deviation of unit drift
electrode_group_name	Name of the electrode group the unit was recorded from
exp_decay	Exponential decay of the autocorrelogram
firing_range	Range of firing rates across the session
firing_rate	Mean spike rate across the whole session (Hz)
half_width	Half-width of the mean spike waveform (s)
is_not_drift	Boolean indicating unit is not classified as a drift artifact
is_qc_pass	Boolean indicating unit passes quality control
isi_violations_count	Number of inter-spike interval violations (<1.5 ms)
isi_violations_ratio	Measure of unit contamination from refractory period violations (default threshold = 0.5)
isolation_distance	Distance to nearest cluster in Mahalanobis space; higher is better
l_ratio	Measure of how separable this unit’s waveforms are from its neighbors’; lower is better
location	brain structure (acronym)
nn_hit_rate	Fraction of spikes with nearest neighbor from same cluster
nn_miss_rate	Measure of fraction of spikes missing from this unit
num_negative_peaks	Number of negative peaks in the mean spike waveform
num_positive_peaks	Number of positive peaks in the mean spike waveform
num_spikes	Total number of spikes detected for the unit
peak_channel	Channel index with the largest amplitude waveform
peak_electrode	Electrode index with the largest amplitude spike waveform
peak_to_valley	Time (s) between waveform peak and trough
peak_trough_ratio	Peak-to-trough ratio of the average spike waveform
presence_ratio	Fraction of the session over which this unit had spikes detected (default threshold = 0.9)
recovery_slope	Slope of the waveform between the trough and the peak (V/s)
repolarization_slope	Slope of the waveform back to 0 after the peak (V/s)
rp_contamination	Estimated contamination from refractory period violations
rp_violations	Number of refractory period violations
silhouette	Measure of unit contamination based on cluster separation
sliding_rp_violation	Sliding refractory period violation metric
snr	Ratio of waveform amplitude relative to background noise on the peak channel
spike_amplitudes	Array of individual spike amplitudes (µV)
spread	Distance the waveform extends above and below the peak channel (µm)
structure	Brain structure acronym where the unit was recorded
sync_spike_2	Synchrony of unit spikes within 2 ms windows
sync_spike_4	Synchrony of unit spikes within 4 ms windows
sync_spike_8	Synchrony of unit spikes within 8 ms windows
unit_id	Unique UUID identifier for the unit
velocity_above	Speed of waveform propagation above the peak channel (V/s)
velocity_below	Speed of waveform propagation below the peak channel (V/s)
spike_times	Timestamps (s) of each detected spike for the unit
obs_intervals	Time intervals during which the unit was observed/recorded
electrode_group	The electrode group that each spike unit came from

units = nwbfile.units[:]
units

	activity_drift	amplitude	amplitude_cutoff	amplitude_cv_median	amplitude_cv_range	amplitude_median	ccf_ap	ccf_dv	ccf_ml	cluster_id	...	structure	sync_spike_2	sync_spike_4	sync_spike_8	unit_id	velocity_above	velocity_below	spike_times	obs_intervals	electrode_group
id
0	0.310182	86.687622	0.002210	0.292047	0.291903	67.860000	4625.0	5100.0	2900.0	0	...	CP	0.034051	0.000097	0.0	759434_2025-02-04_B-0	301.814836	NaN	[20.899214575483686, 21.360979519709296, 22.05...	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x14017...
1	0.175051	251.456230	0.000043	NaN	NaN	124.020000	4625.0	5100.0	2900.0	1	...	CP	0.040819	0.000000	0.0	759434_2025-02-04_B-1	NaN	NaN	[20.57621578030963, 20.593715715032687, 20.804...	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x14017...
2	0.054430	98.420357	0.000126	0.274439	0.277458	72.540000	4675.0	5050.0	2900.0	2	...	CP	0.038799	0.000000	0.0	759434_2025-02-04_B-2	NaN	NaN	[20.31891674006727, 20.34118332367679, 20.5163...	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x14017...
3	0.053826	65.543402	0.000125	NaN	NaN	30.419998	4625.0	5075.0	2900.0	3	...	CP	0.175586	0.000596	0.0	759434_2025-02-04_B-3	NaN	NaN	[33.335501519909634, 33.34220149491789, 33.343...	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x14017...
4	0.086663	59.702768	0.000152	NaN	NaN	28.079998	4625.0	5100.0	2900.0	4	...	CP	0.088795	0.000370	0.0	759434_2025-02-04_B-4	NaN	NaN	[23.240672508219102, 23.24733915001836, 23.250...	[[20.24118369668792, 7025.1210546177235]]	probeB pynwb.ecephys.ElectrodeGroup at 0x14017...
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
2280	0.131299	409.724686	0.002443	0.097417	0.392093	276.120000	3150.0	2150.0	4550.0	267	...	MOs	0.021467	0.000000	0.0	759434_2025-02-04_F-267	605.804791	NaN	[25.087532998134833, 45.13632054470185, 46.167...	[[20.24268545106928, 7025.104241617593]]	probeF pynwb.ecephys.ElectrodeGroup at 0x14017...
2281	0.369669	268.837971	0.000061	NaN	NaN	208.260000	3050.0	1925.0	4450.0	268	...	MOs	0.019299	0.000000	0.0	759434_2025-02-04_F-268	601.837297	NaN	[871.2026272412407, 1988.115019482439, 2331.90...	[[20.24268545106928, 7025.104241617593]]	probeF pynwb.ecephys.ElectrodeGroup at 0x14017...
2282	0.230310	176.375221	0.000160	NaN	NaN	145.080000	3050.0	1925.0	4500.0	269	...	MOs	0.030272	0.000000	0.0	759434_2025-02-04_F-269	396.446107	NaN	[192.23354004343028, 206.68124969396942, 232.1...	[[20.24268545106928, 7025.104241617593]]	probeF pynwb.ecephys.ElectrodeGroup at 0x14017...
2283	0.342890	107.012836	0.000155	NaN	NaN	81.899994	3050.0	1900.0	4450.0	270	...	MOs	0.026730	0.000000	0.0	759434_2025-02-04_F-270	NaN	NaN	[21.059448894478436, 21.195581690580262, 21.30...	[[20.24268545106928, 7025.104241617593]]	probeF pynwb.ecephys.ElectrodeGroup at 0x14017...
2284	0.024032	84.006008	NaN	NaN	NaN	58.499996	3025.0	1825.0	4425.0	271	...	MOs	0.020833	0.000000	0.0	759434_2025-02-04_F-271	406.432666	NaN	[46.588448147390366, 74.87420318776779, 105.17...	[[20.24268545106928, 7025.104241617593]]	probeF pynwb.ecephys.ElectrodeGroup at 0x14017...

2285 rows × 59 columns

Spike times#

The spike_times column contains one array per unit with the times (in seconds, aligned to the session clock) of every detected spike for that unit. This is the main entry point for building rasters, PSTHs, and firing-rate summaries.

spike_times = units.spike_times 
spike_times

id
     [20.899214575483686, 21.360979519709296, 22.05...
     [20.57621578030963, 20.593715715032687, 20.804...
     [20.31891674006727, 20.34118332367679, 20.5163...
     [33.335501519909634, 33.34220149491789, 33.343...
     [23.240672508219102, 23.24733915001836, 23.250...
                              ...                        
  [25.087532998134833, 45.13632054470185, 46.167...
  [871.2026272412407, 1988.115019482439, 2331.90...
  [192.23354004343028, 206.68124969396942, 232.1...
  [21.059448894478436, 21.195581690580262, 21.30...
  [46.588448147390366, 74.87420318776779, 105.17...
Name: spike_times, Length: 2285, dtype: object

Filtering by quality and brain structure#

Two columns are useful for narrowing down units for further analysis:

default_qc: boolean indicating whether the unit passed default quality-control metrics.
structure: the CCF-annotated brain structure the unit is located in.

# Combine and count the structure and default_qc columns to identify the number of good units in each brain structure. 

units.groupby("structure")["default_qc"].agg(passing="sum", total="count").sort_values("passing", ascending=False)

	passing	total
structure
SSp	87	460
MOs	70	598
CP	66	442
TTd	42	87
ILA	32	153
DP	32	117
CA3	25	192
PL	22	108
CA1	8	47
OLF	3	8
VISli	2	22
TEa	2	16
ACAd	1	7
DG	1	2
scwm	1	1
VISl	0	2
STR	0	5
ccb	0	4
out of brain	0	14

Session epochs#

Each session is divided into a few high-level epochs (eg. receptive field mapping, spontaneous, dynamic routing task). These are stored in the epochs intervals table and provide the time boundaries for each epoch.

Column	Description
start_time	start time of epoch (s)
stop_time	stop time of epoch (s)
script_name	the name of the TaskControl subclass that controlled stimulus presentation during the epoch
notes	notes about the experiment or the data collected during the epoch
interval_names	names of other intervals tables that contain trial data from the epoch
tags	user-defined tags

epochs = nwbfile.intervals["epochs"].to_dataframe()
epochs.head()

	start_time	stop_time	script_name	interval_names	tags
id
0	45.62740	916.491240	RFMapping	[vis_rf_mapping_trials, aud_rf_mapping_trials]	[mapping]
1	927.69937	1530.872170	Spontaneous	[]	[spontaneous]
2	1541.98091	2145.086620	SpontaneousRewards	[]	[rewards, spontaneous]
3	2155.69515	5796.812075	DynamicRouting1	[trials, performance]	[task, rewards]
4	5806.68705	6409.775485	SpontaneousRewards	[]	[rewards, spontaneous]

Trials#

The Dynamic Routing task behavior is organized around trials. The trials table contains one row per trial with the trial timing and task variables such as stimulus identity, block context, whether a reward was delivered, and the animal’s response. Use it to select trials of interest and align neural data to task events.

Column	Description
start_time	Start time of epoch (s)
stop_time	Stop time of epoch (s)
quiescent_start_time	Start of pre-stimulus interval in which the subject does not lick; only the last quiescent interval (which was not violated) is included
quiescent_stop_time	End of pre-stimulus interval in which the subject does not lick; not equal to `stim_start_time`, which factors in processing and stimulus device latency
stim_start_time	Onset of visual or auditory stimulus
stim_stop_time	Offset of visual or auditory stimulus
response_window_start_time	Start of interval in which the subject should lick if a GO trial, otherwise should not lick
response_window_stop_time	End of interval in which the subject should lick if a GO trial, otherwise should not lick
task_control_response_time	Time of first lick in trial according to the task control script; nan if no response registered
response_time	Time of first lick within the response window; nan if no lick occurred
reward_time	Delivery time of water reward, for contingent and non-contingent rewards
post_response_window_start_time	Start of null interval in which the subject awaits a new trial
post_response_window_stop_time	End of null interval
stim_name	The stimulus presented; corresponds to a unique stimulus definition, randomized over trials
grating_phase	Phase of the visual grating in cycles; 0 or 0.5 for visual stimuli; nan for auditory stimuli
block_index	0-indexed block number, increments with each block
rewarded_modality	Name of the rewarded modality in each block; not an exact correspondence with values in `stim_name`
trial_index	0-indexed trial number
trial_index_in_block	0-indexed trial number within the block
repeat_index	Number of times the trial has already been presented in immediately preceding trials; nan for catch trials
is_response	The subject licked one or more times during the response window
is_correct	The subject acted correctly in the response window; includes correct reject for catch trials
is_incorrect	The subject acted incorrectly in the response window; includes false alarm for catch trials
is_hit	The subject responded in a GO trial
is_false_alarm	The subject responded in a NOGO trial; excludes catch trials
is_correct_reject	The subject did not respond in a NOGO trial; excludes catch trials
is_miss	The subject did not respond in a GO trial
is_go	Condition in which the subject should respond; target stim presented in rewarded block
is_nogo	Condition in which the subject should not respond; excludes catch trials
is_rewarded	The subject received a reward; includes non-contingent rewards
is_noncontingent_reward	The subject received a reward that did not depend on its response
is_contingent_reward	The subject received a reward for a correct response
is_reward_scheduled	A non-contingent reward was scheduled to occur regardless of whether it was delivered
is_instruction	Stimulus specifically chosen to inform the subject of a change in rewarded modality
is_aud_stim	An auditory stimulus was presented; excludes catch trials
is_vis_stim	A visual stimulus was presented; excludes catch trials
is_catch	No stimulus was presented
is_target	A stimulus was presented that the subject should respond to only in a specific block
is_aud_target	An auditory stimulus the subject should respond to only in a specific block
is_vis_target	A visual stimulus the subject should respond to only in a specific block
is_nontarget	A stimulus the subject should never respond to
is_aud_nontarget	An auditory stimulus the subject should never respond to
is_vis_nontarget	A visual stimulus the subject should never respond to
is_vis_rewarded	Visual target stimuli are rewarded
is_aud_rewarded	Auditory target stimuli are rewarded
is_block_switch	The first trial with a stimulus after a change in rewarded modality
is_repeat	The trial is a repetition of the previous trial due to a miss
is_opto	Optogenetic inactivation was applied during the trial
is_task_control_correct	The task control script interpreted the subject’s response correctly; where False, `is_hit` or `is_miss` may be incorrect

trials = nwbfile.trials.to_dataframe()
trials.head()

	start_time	stop_time	quiescent_start_time	quiescent_stop_time	stim_start_time	stim_stop_time	response_window_start_time	response_window_stop_time	task_control_response_time	response_time	...	is_vis_target	is_nontarget	is_aud_nontarget	is_vis_nontarget	is_vis_rewarded	is_aud_rewarded	is_block_switch	is_repeat	is_opto	is_task_control_correct
id
0	2158.88748	2164.39167	2158.88748	2160.35497	2160.415740	2160.916160	2160.47170	2161.38916	2161.07221	2161.06612	...	True	False	False	False	True	False	False	False	False	False
1	2165.30909	2170.81367	2165.30909	2166.77695	2166.837800	2167.338220	2166.89376	2167.81124	2167.22735	2167.21475	...	True	False	False	False	True	False	False	False	False	False
2	2172.76534	2178.28664	2172.76534	2174.23327	2174.294050	2174.794460	2174.34997	2175.26747	2174.60025	2174.59576	...	True	False	False	False	True	False	False	False	False	False
3	2179.65444	2185.17571	2179.65444	2181.12234	2181.183375	2181.683795	2181.23910	2182.15653	2181.47267	2181.46901	...	True	False	False	False	True	False	False	False	False	False
4	2185.29248	2190.81381	2185.29248	2186.76041	2186.821210	2187.321630	2186.87719	2187.79464	2187.09402	2187.09076	...	True	False	False	False	True	False	False	False	False	False

5 rows × 49 columns

Performance#

The performance intervals table summarizes behavioral performance at the block level (rather than per trial), which is useful when comparing behavior across the alternating auditory- and visual-rewarded contexts.

Column	Description
start_time	Start time of epoch (s)
stop_time	Stop time of epoch (s)
block_index	Presentation position of the block in the task (0-indexed)
n_trials	The number of trials in the block
n_responses	The number of responses the subject made in trials in the block
n_hits	The number of correct responses the subject made in GO trials in the block (excluding trials with scheduled reward)
n_contingent_rewards	The number of rewards the subject received for correct responses in the block
hit_rate	The proportion of correct responses the subject made in GO trials in the block (excluding trials with scheduled reward)
false_alarm_rate	The proportion of incorrect responses the subject made in NOGO trials in the block
catch_response_rate	The proportion of responses the subject made in catch trials in the block
rewarded_modality	The modality of the target stimulus that was rewarded in the block: normally `vis` or `aud`
is_first_block_aud	Whether the rewarded modality of the first block in the task was auditory
cross_modality_dprime	dprime across modalities; hits=response rate to rewarded target stimulus, false alarms=response rate to non-rewarded target stimulus
signed_cross_modality_dprime	Same as `cross_modality_dprime` but with negative values for auditory blocks
vis_dprime	dprime within visual modality; hits=response rate to visual target stimulus, false alarms=response rate to visual non-target stimulus
aud_dprime	dprime within auditory modality; hits=response rate to auditory target stimulus, false alarms=response rate to auditory non-target stimulus
vis_target_response_rate	The proportion of responses the subject made to visual target stimulus trials in the block (excluding trials with scheduled reward)
vis_nontarget_response_rate	The proportion of responses the subject made to visual nontarget stimulus trials in the block (excluding trials with scheduled reward)
aud_target_response_rate	The proportion of responses the subject made to auditory target stimulus trials in the block (excluding trials with scheduled reward)
aud_nontarget_response_rate	The proportion of responses the subject made to auditory nontarget stimulus trials in the block (excluding trials with scheduled reward)

performance = nwbfile.intervals["performance"].to_dataframe()
performance.head()

	start_time	stop_time	block_index	n_trials	n_responses	n_hits	n_contingent_rewards	hit_rate	false_alarm_rate	catch_response_rate	rewarded_modality	is_first_block_aud	cross_modality_dprime	signed_cross_modality_dprime	vis_dprime	aud_dprime	vis_target_response_rate	vis_nontarget_response_rate	aud_target_response_rate	aud_nontarget_response_rate
id
0	2158.88748	2763.96067	0	92	25.0	24.0	24.0	1.000000	0.016667	3.125000	vis	False	3.681688	3.681688	3.996798	0.000000	1.000000	0.00	0.05	0.000000
1	2764.91140	3369.10091	1	89	38.0	21.0	21.0	0.954545	0.280702	3.800000	aud	False	1.889823	-1.889823	0.000000	1.889823	0.421053	0.00	1.00	0.421053
2	3369.86822	3976.22623	2	89	26.0	24.0	24.0	0.960000	0.035088	3.714286	vis	False	3.688618	3.688618	3.395540	-0.344713	1.000000	0.05	0.00	0.055556
3	3976.52642	4584.60250	3	89	36.0	23.0	23.0	1.000000	0.228070	4.000000	aud	False	2.498592	-2.498592	-0.293078	2.449813	0.315789	0.05	1.00	0.333333
4	4584.90278	5191.94456	4	93	27.0	25.0	25.0	1.000000	0.032787	3.857143	vis	False	3.698603	3.698603	4.034501	-0.315110	1.000000	0.00	0.05	0.050000

Behavior data#

Along with the task-level tables, each session includes continuous behavioral measurements of running speed, eye tracking, and behavior keypoint tracking collected while the mouse performs the task. These live in the behavior module of the nwbfile.processing.behavior container.

nwbfile.processing['behavior']

description: processed behavior data

data_interfaces

facemap_front_camera

resolution: -1.0

comments: no comments

description: motion SVD for video from front camera; shape is number of frames by number of components (500)

conversion: 1.0

offset: 0.0

unit: pixels

data

Data type	float32
Shape	(420648, 500)
Array size	802.32 MiB

timestamps

Data type	float64
Shape	(420648,)
Array size	3.21 MiB

timestamps_unit: seconds

interval: 1

facemap_side_camera

resolution: -1.0

comments: no comments

description: motion SVD for video from side camera; shape is number of frames by number of components (500)

conversion: 1.0

offset: 0.0

unit: pixels

data

Data type	float32
Shape	(420666, 500)
Array size	802.36 MiB

timestamps

Data type	float64
Shape	(420666,)
Array size	3.21 MiB

timestamps_unit: seconds

interval: 1

running_speed

resolution: -1.0

comments: no comments

description: linear forward running speed on a rotating disk, low-pass filtered at 4 Hz with a 3rd order Butterworth filter

conversion: 1.0

offset: 0.0

unit: cm/s

data

Data type	float64
Shape	(412214,)
Array size	3.14 MiB

timestamps

Data type	float64
Shape	(412214,)
Array size	3.14 MiB

timestamps_unit: seconds

interval: 1

dlc_eye_camera

description: DeepLabCut tracking model fit to each frame of eye camera video. Output for every frame includes: `timestamps`: start time of frame exposure, in seconds | `_x` and `_y`: coordinates in pixels, with (0, 0) at top-left of frame | `_likelihood`: likelihood of the model (softmax output of the deep neural network)

table

	cr1_x	cr10_x	cr11_x	cr12_x	cr2_x	cr3_x	cr4_x	cr5_x	cr6_x	cr7_x	cr8_x	cr9_x	eye1_x	eye10_x	eye11_x	eye12_x	eye2_x	eye3_x	eye4_x	eye5_x	eye6_x	eye7_x	eye8_x	eye9_x	pupil1_x	pupil10_x	pupil11_x	pupil12_x	pupil2_x	pupil3_x	pupil4_x	pupil5_x	pupil6_x	pupil7_x	pupil8_x	pupil9_x	cr1_y	cr10_y	cr11_y	cr12_y	cr2_y	cr3_y	cr4_y	cr5_y	cr6_y	cr7_y	cr8_y	cr9_y	eye1_y	eye10_y	eye11_y	eye12_y	eye2_y	eye3_y	eye4_y	eye5_y	eye6_y	eye7_y	eye8_y	eye9_y	pupil1_y	pupil10_y	pupil11_y	pupil12_y	pupil2_y	pupil3_y	pupil4_y	pupil5_y	pupil6_y	pupil7_y	pupil8_y	pupil9_y	cr1_likelihood	cr10_likelihood	cr11_likelihood	cr12_likelihood	cr2_likelihood	cr3_likelihood	cr4_likelihood	cr5_likelihood	cr6_likelihood	cr7_likelihood	cr8_likelihood	cr9_likelihood	eye1_likelihood	eye10_likelihood	eye11_likelihood	eye12_likelihood	eye2_likelihood	eye3_likelihood	eye4_likelihood	eye5_likelihood	eye6_likelihood	eye7_likelihood	eye8_likelihood	eye9_likelihood	pupil1_likelihood	pupil10_likelihood	pupil11_likelihood	pupil12_likelihood	pupil2_likelihood	pupil3_likelihood	pupil4_likelihood	pupil5_likelihood	pupil6_likelihood	pupil7_likelihood	pupil8_likelihood	pupil9_likelihood	timestamps
id
0	6.257579	3.310695	2.865996	61.524036	55.815071	59.706459	61.820957	60.875648	60.541634	63.163883	57.695103	58.799397	-0.263414	4.733630	2.549963	6.088755	4.848226	3.684231	95.296310	4.485808	42.258923	4.645335	51.154285	5.319347	4.342977	62.903099	0.763001	3.143172	2.420771	52.241173	65.632851	62.905418	63.694363	5.825314	5.661117	4.155485	77.114662	155.906342	153.169983	196.260040	199.712463	205.217072	200.374313	197.969772	201.380676	166.143738	191.948074	192.319366	153.580902	154.360458	159.337479	190.358536	156.354660	3.199129	205.206833	87.183762	202.524109	157.757736	196.787369	153.522400	78.079132	190.232651	73.710930	75.290230	78.191711	188.103439	188.820938	192.818100	185.288879	190.196808	182.250031	155.906448	0.001637	0.001441	0.000855	0.001189	0.003616	0.005150	0.020247	0.014635	0.012463	0.009171	0.006167	0.001744	0.004395	0.008654	0.010360	0.001614	0.002157	0.001984	0.004401	0.021181	0.005255	0.043138	0.013506	0.048915	0.005857	0.002141	0.001750	0.004098	0.006094	0.003936	0.007695	0.036590	0.003669	0.002257	0.003137	0.010067	NaN
1	321.738190	313.308655	319.621552	315.709595	313.172668	311.794983	310.274414	305.894470	309.785889	308.276642	308.806885	308.572418	435.308075	299.091217	277.063324	434.011047	416.929474	356.519714	324.248566	352.675964	154.717300	136.778046	171.753586	242.873734	331.124298	267.789185	330.985229	330.398590	327.712616	5.982954	4.909490	4.479672	11.007477	29.517284	269.723846	59.197319	267.661224	258.497620	263.451752	265.682556	268.126038	268.868011	269.503357	269.664581	268.029297	262.367798	261.225098	259.865906	215.143021	123.420181	115.761391	195.713150	357.691925	382.070068	384.816254	381.832977	308.721130	250.920517	171.384689	132.624466	265.426117	124.009918	261.875458	263.757965	266.179779	1.074963	1.035730	6.395949	7.879985	4.490459	208.451828	5.525383	0.038439	0.022409	0.015992	0.029169	0.056433	0.053797	0.062198	0.064636	0.047505	0.030858	0.040817	0.029235	0.575440	0.291975	0.089464	0.119383	0.123169	0.379497	0.317344	0.221876	0.912202	0.690871	0.910316	0.742060	0.004969	0.001009	0.001312	0.003360	0.003718	0.001416	0.001353	0.002571	0.000785	0.000473	0.000631	0.001547	14.42651
2	321.339233	313.104065	313.038055	315.953217	314.643219	313.339600	310.715576	306.432983	310.157776	308.000031	308.471375	307.492188	433.814331	282.424591	291.929199	434.258972	419.676910	371.832520	388.898865	205.979645	153.302017	135.069824	172.569229	242.949860	332.160889	192.276749	331.313538	331.792633	328.397125	6.246439	302.795410	4.368991	303.455597	302.858582	4.636980	303.039062	267.530762	258.950684	260.975342	265.457855	268.325317	268.275940	267.522369	268.252747	268.295837	263.268402	261.609131	260.756714	203.416702	121.928513	116.586853	196.831039	355.412170	373.842804	387.741333	354.879913	309.012512	252.337418	171.487961	133.594513	265.067596	173.010254	260.328369	262.315063	265.579285	2.334807	262.063416	6.798071	263.110260	259.747894	7.379796	233.996796	0.040932	0.050733	0.021523	0.030052	0.056541	0.058877	0.071839	0.106047	0.094316	0.076004	0.082712	0.059780	0.252804	0.241494	0.057785	0.095871	0.156900	0.208213	0.312420	0.634833	0.948794	0.822546	0.855607	0.557850	0.004287	0.001511	0.001133	0.003181	0.004705	0.001977	0.003380	0.003554	0.001372	0.001260	0.000755	0.003432	14.44318
3	320.579498	312.271912	313.338074	316.113678	315.685242	314.214691	313.581909	307.414032	307.389160	307.397705	308.053680	306.923340	433.599457	282.896301	277.046265	429.949493	420.487152	364.821838	389.565002	209.603027	152.213654	136.723816	171.384888	273.462250	331.925690	193.439545	327.908539	331.754486	327.292725	315.606598	302.930267	4.263856	302.485809	302.591370	300.961761	269.504395	269.681976	259.510651	261.928741	266.307831	269.663605	271.359589	271.690430	271.146210	269.531372	267.166412	262.451233	261.354736	203.594498	122.555626	116.950859	197.983719	354.025482	377.177002	388.720428	356.149689	308.834686	251.446457	172.854584	129.080551	265.852722	172.128601	250.567947	262.067993	265.779053	270.581970	262.373962	6.784337	258.818451	259.939362	251.349075	207.556824	0.058540	0.099322	0.053506	0.055305	0.076487	0.090631	0.121970	0.187120	0.200461	0.178605	0.143599	0.125837	0.254278	0.224820	0.070715	0.080775	0.136161	0.100006	0.325625	0.520847	0.944977	0.791974	0.890303	0.469317	0.004967	0.002007	0.001757	0.003880	0.005543	0.003575	0.006451	0.003002	0.002394	0.002453	0.001643	0.005704	14.45984

... and 420651 more row(s).

eye_tracking

description: Ellipses fit to three features in each frame of the eye video: pupil: perimeter of the pupil | eye: inner perimeter of the eyelid | cr: corneal reflection, a bright spot near the center of the eye which is always smaller than the pupil

table

	cr_center_x	cr_center_y	cr_width	cr_height	cr_phi	cr_average_confidence	cr_area	cr_is_bad_frame	eye_center_x	eye_center_y	eye_width	eye_height	eye_phi	eye_average_confidence	eye_area	eye_is_bad_frame	pupil_center_x	pupil_center_y	pupil_width	pupil_height	pupil_phi	pupil_average_confidence	pupil_area	pupil_is_bad_frame	timestamps
id
0	NaN	NaN	NaN	NaN	NaN	0.006526	NaN	True	NaN	NaN	NaN	NaN	NaN	0.013797	NaN	True	NaN	NaN	NaN	NaN	NaN	0.007274	NaN	True	NaN
1	NaN	NaN	NaN	NaN	NaN	0.040957	NaN	True	292.777818	257.166495	154.694249	131.328813	0.152833	0.447800	75179.288538	False	NaN	NaN	NaN	NaN	NaN	0.001929	NaN	True	14.42651
2	NaN	NaN	NaN	NaN	NaN	0.062446	NaN	True	298.465554	259.710655	162.739762	130.362037	0.269021	0.428760	83202.662797	False	NaN	NaN	NaN	NaN	NaN	0.002546	NaN	True	14.44318
3	NaN	NaN	NaN	NaN	NaN	0.115949	NaN	True	301.227109	262.851161	166.508229	131.346907	0.341447	0.400817	87100.625934	False	NaN	NaN	NaN	NaN	NaN	0.003615	NaN	True	14.45984

... and 420651 more row(s).

licks

description: times at which the subject made contact with a combined lick sensor + water spout: putatively the starts of licks, but may include other events such as grooming

table

	timestamps	duration	is_likely_lick
id
0	1533.28359	0.04925	True
1	1533.39764	0.03524	True
2	1534.64212	0.08325	True
3	1534.75918	0.07025	True

... and 2349 more row(s).

lp_front_camera

description: Lightning Pose tracking model fit to 12 facial features for each frame of front camera video. Output for every frame includes: `timestamps`: start time of frame exposure, in seconds | `_x` and `_y`: coordinates in pixels, with (0, 0) at top-left of frame | `_likelihood`: keypoint prediction likelihood between 0 and 1, with higher values representing greater confidence of the model | `_pca_error`: Euclidean distance in pixels between the original keypoint prediction and its prediction after projection to and from PCA space | `_temporal_norm`: Euclidean distance in pixels between keypoint predictions on successive time bins. See original publication for further details: https://doi.org/10.1038/s41592-024-02319-1

table

	ear_base_l_likelihood	ear_base_l_pca_error	ear_base_l_temporal_norm	ear_base_l_x	ear_base_l_y	ear_tip_l_likelihood	ear_tip_l_pca_error	ear_tip_l_temporal_norm	ear_tip_l_x	ear_tip_l_y	eye_bottom_l_likelihood	eye_bottom_l_pca_error	eye_bottom_l_temporal_norm	eye_bottom_l_x	eye_bottom_l_y	eye_top_l_likelihood	eye_top_l_pca_error	eye_top_l_temporal_norm	eye_top_l_x	eye_top_l_y	jaw_likelihood	jaw_pca_error	jaw_temporal_norm	jaw_x	jaw_y	nose_tip_likelihood	nose_tip_pca_error	nose_tip_temporal_norm	nose_tip_x	nose_tip_y	nostril_l_likelihood	nostril_l_pca_error	nostril_l_temporal_norm	nostril_l_x	nostril_l_y	tongue_base_l_likelihood	tongue_base_l_pca_error	tongue_base_l_temporal_norm	tongue_base_l_x	tongue_base_l_y	tongue_tip_likelihood	tongue_tip_pca_error	tongue_tip_temporal_norm	tongue_tip_x	tongue_tip_y	whisker_pad_l_side_likelihood	whisker_pad_l_side_pca_error	whisker_pad_l_side_temporal_norm	whisker_pad_l_side_x	whisker_pad_l_side_y	whisker_pad_l_top_likelihood	whisker_pad_l_top_pca_error	whisker_pad_l_top_temporal_norm	whisker_pad_l_top_x	whisker_pad_l_top_y	timestamps
id
0	0.000136	109.305099	NaN	314.509033	214.964294	0.000172	112.505379	NaN	327.771851	236.113205	0.000122	95.341949	NaN	315.893616	218.793091	0.000139	153.173904	NaN	347.803619	251.166504	0.000169	NaN	NaN	325.692200	243.350540	0.000177	108.735733	NaN	333.152832	244.681915	0.000142	109.330887	NaN	348.895142	256.752350	0.000169	21.836403	NaN	322.884949	247.132492	0.000179	19.428129	NaN	324.289337	246.712814	0.000152	113.855881	NaN	332.498230	243.779175	0.000153	94.381584	NaN	326.739655	240.801239	NaN
1	0.988053	108.866219	112.602974	419.982544	175.533737	0.972307	107.616699	152.396545	450.785309	146.155457	0.994750	102.556816	35.129623	343.112091	196.583969	0.999940	113.204994	76.011208	335.016510	176.238586	0.000171	NaN	0.251405	325.929718	243.432938	0.998823	81.456367	61.697796	273.806396	261.552551	0.993623	66.272217	61.125271	287.769958	256.855408	0.000394	21.391623	5.076637	317.808685	247.194077	0.000154	11.067987	1.821925	326.105865	246.852936	0.996880	107.937508	18.800714	316.760559	233.493622	0.999953	76.962456	27.115084	308.014008	221.190582	14.64815
2	0.994776	108.198898	1.337913	419.241333	176.647568	0.951950	106.964584	1.372030	451.922363	146.923294	0.999444	102.852501	0.658990	342.527039	196.887253	0.999919	113.841293	0.104304	335.117584	176.264343	0.000171	NaN	0.013575	325.942413	243.437744	0.999682	78.570297	3.867516	270.299805	259.921143	0.996092	64.747559	2.752445	285.018280	256.920349	0.000303	21.293278	1.256627	316.664948	247.714630	0.000153	10.681618	1.644859	324.593475	247.499649	0.999597	108.049652	1.690798	315.190399	234.120834	0.998654	77.097771	0.746137	307.282532	221.043396	14.66481
3	0.981099	109.902542	2.212809	421.370148	176.043686	0.971989	108.579208	2.934833	452.630219	144.075104	0.999574	102.235023	0.246029	342.363464	196.703476	0.999908	114.072304	0.302804	335.420380	176.266678	0.000171	NaN	0.042453	325.940369	243.395340	0.998286	81.069862	3.134591	273.171234	261.178345	0.999583	67.042244	2.791916	287.490326	258.217957	0.000386	21.582983	2.758146	314.507233	249.432663	0.000153	11.029763	2.003517	326.456024	246.761414	0.997225	108.192528	1.805767	316.885529	233.498474	0.998660	76.209915	0.386780	307.018433	220.760818	14.68148

... and 420644 more row(s).

lp_side_camera

description: Lightning Pose tracking model fit to 11 facial features for each frame of side camera video. Output for every frame includes: `timestamps`: start time of frame exposure, in seconds | `_x` and `_y`: coordinates in pixels, with (0, 0) at top-left of frame | `_likelihood`: keypoint prediction likelihood between 0 and 1, with higher values representing greater confidence of the model | `_pca_error`: Euclidean distance in pixels between the original keypoint prediction and its prediction after projection to and from PCA space | `_temporal_norm`: Euclidean distance in pixels between keypoint predictions on successive time bins. See original publication for further details: https://doi.org/10.1038/s41592-024-02319-1

table

	ear_base_l_likelihood	ear_base_l_pca_error	ear_base_l_temporal_norm	ear_base_l_x	ear_base_l_y	ear_tip_l_likelihood	ear_tip_l_pca_error	ear_tip_l_temporal_norm	ear_tip_l_x	ear_tip_l_y	eye_bottom_l_likelihood	eye_bottom_l_pca_error	eye_bottom_l_temporal_norm	eye_bottom_l_x	eye_bottom_l_y	eye_top_l_likelihood	eye_top_l_pca_error	eye_top_l_temporal_norm	eye_top_l_x	eye_top_l_y	jaw_likelihood	jaw_pca_error	jaw_temporal_norm	jaw_x	jaw_y	nose_tip_likelihood	nose_tip_pca_error	nose_tip_temporal_norm	nose_tip_x	nose_tip_y	nostril_l_likelihood	nostril_l_pca_error	nostril_l_temporal_norm	nostril_l_x	nostril_l_y	tongue_base_l_likelihood	tongue_base_l_pca_error	tongue_base_l_temporal_norm	tongue_base_l_x	tongue_base_l_y	tongue_tip_likelihood	tongue_tip_pca_error	tongue_tip_temporal_norm	tongue_tip_x	tongue_tip_y	whisker_pad_l_side_likelihood	whisker_pad_l_side_pca_error	whisker_pad_l_side_temporal_norm	whisker_pad_l_side_x	whisker_pad_l_side_y	whisker_pad_l_top_likelihood	whisker_pad_l_top_pca_error	whisker_pad_l_top_temporal_norm	whisker_pad_l_top_x	whisker_pad_l_top_y	timestamps
id
0	0.000168	113.267677	NaN	333.837036	246.252258	0.000165	79.879768	NaN	320.156891	243.217575	0.999803	254.468170	NaN	650.118225	486.369476	0.000017	166.664566	NaN	610.629272	458.189606	0.000160	NaN	NaN	336.275818	242.255692	0.000163	191.183212	NaN	340.532349	239.847870	0.000160	205.411041	NaN	354.644165	239.761612	0.000164	49.634796	NaN	327.532043	241.328751	0.000165	39.109268	NaN	326.956726	241.676346	0.002613	109.493004	NaN	648.755249	153.953262	0.000008	184.805695	NaN	633.057129	423.356537	NaN
1	0.998660	19.148771	140.131393	220.169662	164.297791	0.967683	6.152155	137.327957	225.122482	144.084183	0.998860	21.212503	586.085327	168.429596	152.495071	0.999748	15.346764	544.447571	165.611420	144.530197	0.989995	NaN	182.014877	163.617432	184.649292	0.996758	19.653793	215.132629	136.279358	172.299652	0.999060	13.091238	223.260513	141.179794	174.353531	0.000136	57.599781	23.602236	304.292969	237.204315	0.000078	10.939700	92.018845	238.447937	216.503693	0.999985	44.217010	493.850677	155.161819	169.890945	0.999715	13.460671	547.459656	151.391129	163.145294	14.19090
2	0.998240	16.902878	1.914873	218.254791	164.295212	0.939089	6.250778	0.101881	225.024612	144.055878	0.997475	20.620049	0.258640	168.633972	152.653580	0.999507	13.601815	0.215744	165.710876	144.721649	0.993864	NaN	0.637287	163.055664	184.950211	0.996525	18.983356	0.148255	136.160416	172.211151	0.998986	12.116210	0.101311	141.197617	174.253799	0.000125	49.693466	16.330482	289.068665	231.296249	0.000076	7.766047	5.381122	233.339066	214.813751	0.999973	40.651848	0.202028	155.162720	170.092972	0.999431	11.975651	0.162747	151.438599	163.300964	14.20756
3	0.999538	19.867174	1.068522	217.237686	163.967743	0.991282	10.473170	1.310066	224.011932	143.224762	0.999953	26.064354	0.535453	168.833847	153.150330	0.998141	16.130512	0.469745	165.988861	145.100311	0.985022	NaN	0.577968	163.633423	184.934647	0.997510	24.649723	0.114425	136.125870	172.102066	0.999287	15.488349	0.151104	141.086517	174.151382	0.000143	49.942989	20.518162	308.121674	238.910568	0.000130	14.331257	52.997490	283.749512	231.169815	0.999961	52.588783	0.259248	155.409256	170.173157	0.999686	13.902470	0.186598	151.563370	163.439713	14.22423

... and 420662 more row(s).

quiescent_interval_violations

description: times at which the subject made contact with the lick spout during a pre-trial quiescent interval, triggering a restart of the trial

table

	timestamps
id
0	2600.32356
1	2602.02498
2	2785.17845
3	2797.55546

... and 25 more row(s).

rewards

description: water rewards delivered to the subject

table

	timestamps	duration	is_solenoid_time
id
0	1632.19683	0.04145	True
1	1722.70581	0.05076	True
2	1813.21498	0.04144	True
3	1903.72414	0.04141	True

... and 152 more row(s).

Running speed#

The mouse is head-fixed on a running wheel and is free to run throughout the session. An encoder on the wheel provides a continuous running-speed time series.

running = nwbfile.processing['behavior']['running_speed'].data[:]
running_timestamps = nwbfile.processing['behavior']['running_speed'].timestamps[:]

Eye tracking#

Eye tracking uses information about the eye, the pupil, and a corneal reflection (CR) of an IR LED to estimate the position and area of the pupil over the course of the session. Because there is one row per video frame, the table can be large; slicing it to a few rows is a quick way to see the available columns.

Column	Description
cr_center_x	Center of the corneal reflection x position
cr_center_y	Center of the corneal reflection y position
cr_width	Width of the corneal reflection
cr_height	Height of the corneal reflection
cr_phi	Rotation angle of the corneal reflection ellipse relative to horizontal-axis of video, in radians
cr_average_confidence	Mean confidence [0-1] for the up-to-12 points from DLC used to fit corneal reflection ellipse
cr_area	Area of the corneal reflection
cr_is_bad_frame	Flag indicating the corneal reflection fit is unreliable for this frame
eye_center_x	Center of the eye x position
eye_center_y	Center of the eye y position
eye_width	Width of the eye
eye_height	Height of the eye
eye_phi	Rotation angle of the eye ellipse relative to horizontal-axis of video, in radians
eye_average_confidence	Mean confidence [0-1] for the up-to-12 points from DLC used to fit eye ellipse
eye_area	Area of the eye
eye_is_bad_frame	Flag indicating the eye ellipse fit is unreliable for this frame
pupil_center_x	Center of the pupil x position
pupil_center_y	Center of the pupil y position
pupil_width	Width of the pupil
pupil_height	Height of the pupil
pupil_phi	Rotation angle of the pupil ellipse relative to horizontal-axis of video, in radians
pupil_average_confidence	Mean confidence [0-1] for the up-to-12 points from DLC used to fit pupil ellipse
pupil_area	Area of the pupil
pupil_is_bad_frame	Flag indicating the pupil ellipse fit is unreliable for this frame
timestamps	Timestamps for all other series

eye_tracking = nwbfile.processing['behavior']['eye_tracking'][0:10] # large table, so just getting the first 10 rows 
eye_tracking

	cr_center_x	cr_center_y	cr_width	cr_height	cr_phi	cr_average_confidence	cr_area	cr_is_bad_frame	eye_center_x	eye_center_y	...	eye_is_bad_frame	pupil_center_x	pupil_center_y	pupil_width	pupil_height	pupil_phi	pupil_average_confidence	pupil_area	pupil_is_bad_frame	timestamps
id
0	NaN	NaN	NaN	NaN	NaN	0.006526	NaN	True	NaN	NaN	...	True	NaN	NaN	NaN	NaN	NaN	0.007274	NaN	True	NaN
1	NaN	NaN	NaN	NaN	NaN	0.040957	NaN	True	292.777818	257.166495	...	False	NaN	NaN	NaN	NaN	NaN	0.001929	NaN	True	14.42651
2	NaN	NaN	NaN	NaN	NaN	0.062446	NaN	True	298.465554	259.710655	...	False	NaN	NaN	NaN	NaN	NaN	0.002546	NaN	True	14.44318
3	NaN	NaN	NaN	NaN	NaN	0.115949	NaN	True	301.227109	262.851161	...	False	NaN	NaN	NaN	NaN	NaN	0.003615	NaN	True	14.45984
4	NaN	NaN	NaN	NaN	NaN	0.118731	NaN	True	298.783399	261.915275	...	False	NaN	NaN	NaN	NaN	NaN	0.004573	NaN	True	14.47651
5	NaN	NaN	NaN	NaN	NaN	0.103269	NaN	True	299.359589	262.008616	...	False	NaN	NaN	NaN	NaN	NaN	0.004557	NaN	True	14.49317
6	NaN	NaN	NaN	NaN	NaN	0.110515	NaN	True	300.013752	260.932320	...	False	NaN	NaN	NaN	NaN	NaN	0.004408	NaN	True	14.50984
7	NaN	NaN	NaN	NaN	NaN	0.108935	NaN	True	302.067252	259.293426	...	False	NaN	NaN	NaN	NaN	NaN	0.005164	NaN	True	14.52651
8	NaN	NaN	NaN	NaN	NaN	0.139220	NaN	True	303.438215	258.568456	...	False	NaN	NaN	NaN	NaN	NaN	0.005924	NaN	True	14.54317
9	NaN	NaN	NaN	NaN	NaN	0.133491	NaN	True	302.728352	257.803906	...	False	NaN	NaN	NaN	NaN	NaN	0.005993	NaN	True	14.55984

10 rows × 25 columns

Behavior keypoint tracking#

Keypoint tracking uses Lightning Pose on video from a front and a side camera to track anatomical landmarks (ear, nose, whisker pad, etc.) over the session. Each camera produces its own table with one row per video frame.

Column	Description
ear_base_l_x	Left ear base x coordinate (px)
ear_base_l_y	Left ear base y coordinate (px)
ear_base_l_likelihood	Left ear base model confidence [0-1]
ear_base_l_pca_error	Left ear base PCA error (px)
ear_base_l_temporal_norm	Left ear base temporal norm (px)
ear_tip_l_x	Left ear tip x coordinate (px)
ear_tip_l_y	Left ear tip y coordinate (px)
ear_tip_l_likelihood	Left ear tip model confidence [0-1]
ear_tip_l_pca_error	Left ear tip PCA error (px)
ear_tip_l_temporal_norm	Left ear tip temporal norm (px)
eye_bottom_l_x	Left eye bottom x coordinate (px)
eye_bottom_l_y	Left eye bottom y coordinate (px)
eye_bottom_l_likelihood	Left eye bottom model confidence [0-1]
eye_bottom_l_pca_error	Left eye bottom PCA error (px)
eye_bottom_l_temporal_norm	Left eye bottom temporal norm (px)
eye_top_l_x	Left eye top x coordinate (px)
eye_top_l_y	Left eye top y coordinate (px)
eye_top_l_likelihood	Left eye top model confidence [0-1]
eye_top_l_pca_error	Left eye top PCA error (px)
eye_top_l_temporal_norm	Left eye top temporal norm (px)
jaw_x	Jaw x coordinate (px)
jaw_y	Jaw y coordinate (px)
jaw_likelihood	Jaw model confidence [0-1]
jaw_pca_error	Jaw PCA error (px)
jaw_temporal_norm	Jaw temporal norm (px)
nose_tip_x	Nose tip x coordinate (px)
nose_tip_y	Nose tip y coordinate (px)
nose_tip_likelihood	Nose tip model confidence [0-1]
nose_tip_pca_error	Nose tip PCA error (px)
nose_tip_temporal_norm	Nose tip temporal norm (px)
nostril_l_x	Left nostril x coordinate (px)
nostril_l_y	Left nostril y coordinate (px)
nostril_l_likelihood	Left nostril model confidence [0-1]
nostril_l_pca_error	Left nostril PCA error (px)
nostril_l_temporal_norm	Left nostril temporal norm (px)
tongue_base_l_x	Left tongue base x coordinate (px)
tongue_base_l_y	Left tongue base y coordinate (px)
tongue_base_l_likelihood	Left tongue base model confidence [0-1]
tongue_base_l_pca_error	Left tongue base PCA error (px)
tongue_base_l_temporal_norm	Left tongue base temporal norm (px)
tongue_tip_x	Tongue tip x coordinate (px)
tongue_tip_y	Tongue tip y coordinate (px)
tongue_tip_likelihood	Tongue tip model confidence [0-1]
tongue_tip_pca_error	Tongue tip PCA error (px)
tongue_tip_temporal_norm	Tongue tip temporal norm (px)
whisker_pad_l_side_x	Left whisker pad side x coordinate (px)
whisker_pad_l_side_y	Left whisker pad side y coordinate (px)
whisker_pad_l_side_likelihood	Left whisker pad side model confidence [0-1]
whisker_pad_l_side_pca_error	Left whisker pad side PCA error (px)
whisker_pad_l_side_temporal_norm	Left whisker pad side temporal norm (px)
whisker_pad_l_top_x	Left whisker pad top x coordinate (px)
whisker_pad_l_top_y	Left whisker pad top y coordinate (px)
whisker_pad_l_top_likelihood	Left whisker pad top model confidence [0-1]
whisker_pad_l_top_pca_error	Left whisker pad top PCA error (px)
whisker_pad_l_top_temporal_norm	Left whisker pad top temporal norm (px)
timestamps	Frame exposure start time (s)

front_camera = nwbfile.processing['behavior']['lp_front_camera'][0:10] # taking a small slice of the table to display 
front_camera

	ear_base_l_likelihood	ear_base_l_pca_error	ear_base_l_temporal_norm	ear_base_l_x	ear_base_l_y	ear_tip_l_likelihood	ear_tip_l_pca_error	ear_tip_l_temporal_norm	ear_tip_l_x	ear_tip_l_y	...	whisker_pad_l_side_pca_error	whisker_pad_l_side_temporal_norm	whisker_pad_l_side_x	whisker_pad_l_side_y	whisker_pad_l_top_likelihood	whisker_pad_l_top_pca_error	whisker_pad_l_top_temporal_norm	whisker_pad_l_top_x	whisker_pad_l_top_y	timestamps
id
0	0.000136	109.305099	NaN	314.509033	214.964294	0.000172	112.505379	NaN	327.771851	236.113205	...	113.855881	NaN	332.498230	243.779175	0.000153	94.381584	NaN	326.739655	240.801239	NaN
1	0.988053	108.866219	112.602974	419.982544	175.533737	0.972307	107.616699	152.396545	450.785309	146.155457	...	107.937508	18.800714	316.760559	233.493622	0.999953	76.962456	27.115084	308.014008	221.190582	14.64815
2	0.994776	108.198898	1.337913	419.241333	176.647568	0.951950	106.964584	1.372030	451.922363	146.923294	...	108.049652	1.690798	315.190399	234.120834	0.998654	77.097771	0.746137	307.282532	221.043396	14.66481
3	0.981099	109.902542	2.212809	421.370148	176.043686	0.971989	108.579208	2.934833	452.630219	144.075104	...	108.192528	1.805767	316.885529	233.498474	0.998660	76.209915	0.386780	307.018433	220.760818	14.68148
4	0.985794	108.618919	0.730171	422.070435	175.836929	0.964218	107.511787	2.359758	451.809570	146.287567	...	107.920067	0.554303	317.141602	233.006866	0.999568	76.376831	0.614517	307.605255	220.578415	14.69815
5	0.994461	109.095413	1.611695	421.305511	177.255539	0.979128	107.779579	0.223019	451.841522	146.066849	...	107.791252	0.934144	317.630280	232.210739	0.998033	76.076538	0.763619	307.503021	219.821671	14.71481
6	0.995578	107.994415	0.938925	421.914246	176.540680	0.981624	106.795395	2.411428	452.020599	148.471619	...	107.529922	1.920599	315.954437	233.148956	0.999416	75.978951	0.950534	306.901947	220.558029	14.73148
7	0.990939	108.525406	0.579094	421.958405	175.963272	0.930161	107.448532	1.789298	451.991547	146.682556	...	108.544914	1.044766	316.659058	233.920349	0.997225	76.289452	0.601790	307.502472	220.519028	14.74814
8	0.991479	109.543335	0.940580	421.020203	176.030121	0.996581	108.356750	1.151731	451.708801	145.566071	...	107.930389	0.816996	316.345490	233.165924	0.997671	76.209831	0.031022	307.477783	220.500244	14.76481
9	0.998907	109.375648	0.489749	420.730530	176.425018	0.988270	108.065475	0.839152	451.031281	146.061188	...	107.478630	0.258242	316.524994	232.980270	0.999978	76.635384	0.659827	307.703857	221.120132	14.78148

10 rows × 56 columns

side_camera = nwbfile.processing['behavior']['lp_side_camera'][0:10] 
side_camera

	ear_base_l_likelihood	ear_base_l_pca_error	ear_base_l_temporal_norm	ear_base_l_x	ear_base_l_y	ear_tip_l_likelihood	ear_tip_l_pca_error	ear_tip_l_temporal_norm	ear_tip_l_x	ear_tip_l_y	...	whisker_pad_l_side_pca_error	whisker_pad_l_side_temporal_norm	whisker_pad_l_side_x	whisker_pad_l_side_y	whisker_pad_l_top_likelihood	whisker_pad_l_top_pca_error	whisker_pad_l_top_temporal_norm	whisker_pad_l_top_x	whisker_pad_l_top_y	timestamps
id
0	0.000168	113.267677	NaN	333.837036	246.252258	0.000165	79.879768	NaN	320.156891	243.217575	...	109.493004	NaN	648.755249	153.953262	0.000008	184.805695	NaN	633.057129	423.356537	NaN
1	0.998660	19.148771	140.131393	220.169662	164.297791	0.967683	6.152155	137.327957	225.122482	144.084183	...	44.217010	493.850677	155.161819	169.890945	0.999715	13.460671	547.459656	151.391129	163.145294	14.19090
2	0.998240	16.902878	1.914873	218.254791	164.295212	0.939089	6.250778	0.101881	225.024612	144.055878	...	40.651848	0.202028	155.162720	170.092972	0.999431	11.975651	0.162747	151.438599	163.300964	14.20756
3	0.999538	19.867174	1.068522	217.237686	163.967743	0.991282	10.473170	1.310066	224.011932	143.224762	...	52.588783	0.259248	155.409256	170.173157	0.999686	13.902470	0.186598	151.563370	163.439713	14.22423
4	0.998157	21.190111	1.483017	215.807373	163.575897	0.952091	12.157774	0.727006	223.289917	143.309799	...	57.275726	0.218125	155.205444	170.250870	0.999691	14.799457	0.063464	151.555130	163.502640	14.24090
5	0.999577	19.893827	1.885730	217.609879	164.129929	0.980309	9.985878	2.482976	225.417419	144.589996	...	51.174419	0.151833	155.098679	170.142914	0.999492	13.837907	0.252490	151.411942	163.294678	14.25756
6	0.999483	19.266750	1.241381	218.796051	164.496017	0.998370	9.069194	2.284853	227.347473	145.812881	...	48.310459	0.053690	155.045715	170.151718	0.999466	13.444413	0.127135	151.284836	163.297424	14.27423
7	0.999960	21.868147	0.749405	218.600418	163.772598	0.986393	13.328960	0.948349	227.028671	144.919724	...	58.970863	0.272365	155.233627	170.348877	0.999840	15.359644	0.248939	151.437332	163.494186	14.29090
8	0.998795	20.873512	0.380976	218.239441	163.650787	0.986750	11.333743	2.604463	224.735260	143.685425	...	54.916252	0.313007	154.953735	170.208755	0.999938	14.560589	0.178571	151.299255	163.380951	14.30756
9	0.999782	19.182312	1.149869	219.292526	163.189041	0.995931	6.760922	4.493243	221.462494	140.606750	...	46.078728	0.197744	154.797928	170.086990	0.999741	13.188193	0.238848	151.131866	163.210571	14.32423

10 rows × 56 columns

Accessing Dynamic Routing data

Contents

Accessing Dynamic Routing data#

Loading a session#

root (NWBFile)

Units#

Spike times#

Filtering by quality and brain structure#

Session epochs#

Trials#

Performance#

Behavior data#

behavior (ProcessingModule)

Running speed#

Eye tracking#

Behavior keypoint tracking#