import pynwb
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
Getting data from a session#
We’re going to examine the data available for a single session. We load this using pynwb. This loads all of the data available for this session.
nwb_path = r'/data/222426_2016-02-04_10-25-24_nwb_2026-08-19_17-50-08/222426_2016-02-04_10-25-24_nwb_2026-08-19_17-50-08.nwb.zarr'
nwbfile = pynwb.read_nwb(nwb_path)
nwbfile
root (NWBFile)
session_description: Auto-generated by neuroconv
identifier: 211c0e3c-4b28-4375-b539-cdb71a42851b
session_start_time
2016-02-04 10:25:24-08:00timestamps_reference_time
2016-02-04 10:25:24-08:00file_create_date
0
2024-03-19 15:55:50.497145-04:00stimulus
natural_movie_one_stimulus
resolution: -1.0
comments: no comments
description: The order and timing for presentation of frames from the the natural movie templates.
conversion: 1.0
offset: 0.0
unit: N/A
data
| Data type | uint32 |
|---|---|
| Shape | (9000,) |
| Array size | 35.16 KiB |
timestamps
| Data type | float64 |
|---|---|
| Shape | (9000,) |
| Array size | 70.31 KiB |
timestamps_unit: seconds
interval: 1
indexed_timeseries
starting_time: nan
rate: nan
resolution: -1.0
comments: no comments
description: A natural movie presented to the subject.
conversion: 1.0
offset: 0.0
unit: n.a.
data
| Data type | uint8 |
|---|---|
| Shape | (900, 304, 608) |
| Array size | 158.64 MiB |
starting_time_unit: seconds
device
description: An ASUS PA248Q monitor used to display visual stimuli.
manufacturer: ASUS
natural_scenes_stimulus
resolution: -1.0
comments: no comments
description: The order and timing for presentation of the natural scene templates.
conversion: 1.0
offset: 0.0
unit: N/A
data
| Data type | uint32 |
|---|---|
| Shape | (5950,) |
| Array size | 23.24 KiB |
timestamps
| Data type | float64 |
|---|---|
| Shape | (5950,) |
| Array size | 46.48 KiB |
timestamps_unit: seconds
interval: 1
indexed_timeseries
starting_time: nan
rate: nan
resolution: -1.0
comments: no comments
description: A collection of natural scenes presented to the subject. Lasted for exactly 7 frames.
conversion: 1.0
offset: 0.0
unit: n.a.
data
| Data type | uint8 |
|---|---|
| Shape | (118, 918, 1174) |
| Array size | 121.28 MiB |
starting_time_unit: seconds
device
description: An ASUS PA248Q monitor used to display visual stimuli.
manufacturer: ASUS
spontaneous_stimulus
description: Mean luminance gray image.
table
| start_time | stop_time | |
|---|---|---|
| id | ||
| 0 | 1047.42969 | 1342.66703 |
static_gratings
description: Parameterizations of visual non-moving gratings shown to the subject.
table
| start_time | stop_time | orientation_in_degrees | spatial_frequency_in_cycles_per_degree | phase | is_blank_sweep | |
|---|---|---|---|---|---|---|
| id | ||||||
| 0 | 51.55381 | 51.80381 | 90.0 | 0.04 | 0.5 | False |
| 1 | 51.78653 | 52.03653 | 150.0 | 0.04 | 0.5 | False |
| 2 | 52.05250 | 52.30250 | 30.0 | 0.02 | 0.0 | False |
| 3 | 52.28523 | 52.53523 | 0.0 | 0.32 | 0.5 | False |
... and 5996 more row(s).
stimulus_template
natural_movie_one
starting_time: nan
rate: nan
resolution: -1.0
comments: no comments
description: A natural movie presented to the subject.
conversion: 1.0
offset: 0.0
unit: n.a.
data
| Data type | uint8 |
|---|---|
| Shape | (900, 304, 608) |
| Array size | 158.64 MiB |
starting_time_unit: seconds
device
description: An ASUS PA248Q monitor used to display visual stimuli.
manufacturer: ASUS
natural_scenes_template
starting_time: nan
rate: nan
resolution: -1.0
comments: no comments
description: A collection of natural scenes presented to the subject. Lasted for exactly 7 frames.
conversion: 1.0
offset: 0.0
unit: n.a.
data
| Data type | uint8 |
|---|---|
| Shape | (118, 918, 1174) |
| Array size | 121.28 MiB |
starting_time_unit: seconds
device
description: An ASUS PA248Q monitor used to display visual stimuli.
manufacturer: ASUS
processing
behavior
description: Processed behavioral data.
data_interfaces
BehavioralTimeSeries
time_series
running_speed
resolution: -1.0
comments: no comments
description: Velocity of the subject over time. Mice were positioned on a running disk during the imaging sessions, and a magnetic shaft encoder (US Digital) attached to this disk recorded the running speed of the mouse during the experiment at 60 samples per second. The running speed was down-sampled to match the timing of the 2-photon imaging (30 Hz).
conversion: 1.0
offset: 0.0
unit: cm/s
data
| Data type | float32 |
|---|---|
| Shape | (113723,) |
| Array size | 444.23 KiB |
timestamps
| Data type | float64 |
|---|---|
| Shape | (113723,) |
| Array size | 888.46 KiB |
timestamps_unit: seconds
interval: 1
ophys
description: Contains processed optical physiology data.
data_interfaces
DfOverF
roi_response_series
DfOverF
resolution: -1.0
comments: no comments
description: The normalized ΔF/F trace calculated using the AllenSDK. Please consult the AllenSDK for details of the calculation.
conversion: 1.0
offset: 0.0
unit: a.u.
data
| Data type | float32 |
|---|---|
| Shape | (113888, 174) |
| Array size | 75.59 MiB |
timestamps (link to processing/ophys/Fluorescence/Corrected/timestamps)
| Data type | float64 |
|---|---|
| Shape | (113888,) |
| Array size | 889.75 KiB |
timestamps_unit: seconds
interval: 1
rois
description: The regions of interest (ROIs) this response series refers to.
table
description: Segmented regions of interest (ROI).
imaging_plane
optical_channel
0
description: An optical channel used to collection light emission during two-photon calcium imaging.
emission_lambda: nan
description: The imaging plane sampled by the two-photon calcium imaging at a depth of {depth} µm.
device
description: A Nikon A1R-MP multiphoton microscope. This system was adapted to provide space to accommodate the behavior apparatus.
manufacturer: Nikon
excitation_lambda: 910.0
indicator: GCaMP6f
location: VISp
conversion: 1.0
unit: meters
origin_coords_unit: meters
grid_spacing
| Data type | float64 |
|---|---|
| Shape | (2,) |
| Array size | 16.00 bytes |
[0.78 0.78]
grid_spacing_unit: micrometers
table
| global_roi_id | pixel_mask | |
|---|---|---|
| id | ||
| 517473350 | 517473350 | [[55, 291, 1.0], [55, 292, 1.0], [56, 290, 1.0], [56, 291, 1.0], [56, 292, 1.0], [56, 293, 1.0], [56, 294, 1.0], [56, 295, 1.0], [56, 296, 1.0], [57, 289, 1.0], [57, 290, 1.0], [57, 291, 1.0], [57, 292, 1.0], [57, 293, 1.0], [57, 294, 1.0], [57, 295, 1.0], [57, 296, 1.0], [57, 297, 1.0], [57, 298, 1.0], [58, 288, 1.0], [58, 289, 1.0], [58, 290, 1.0], [58, 291, 1.0], [58, 292, 1.0], [58, 293, 1.0], [58, 294, 1.0], [58, 295, 1.0], [58, 296, 1.0], [58, 297, 1.0], [58, 298, 1.0], [58, 299, 1.0], [59, 288, 1.0], [59, 289, 1.0], [59, 290, 1.0], [59, 291, 1.0], [59, 292, 1.0], [59, 293, 1.0], [59, 294, 1.0], [59, 295, 1.0], [59, 296, 1.0], [59, 297, 1.0], [59, 298, 1.0], [59, 299, 1.0], [60, 288, 1.0], [60, 289, 1.0], [60, 290, 1.0], [60, 291, 1.0], [60, 292, 1.0], [60, 293, 1.0], [60, 294, 1.0], [60, 295, 1.0], [60, 296, 1.0], [60, 297, 1.0], [60, 298, 1.0], [60, 299, 1.0], [61, 287, 1.0], [61, 288, 1.0], [61, 289, 1.0], [61, 290, 1.0], [61, 291, 1.0], [61, 292, 1.0], [61, 293, 1.0], [61, 294, 1.0], [61, 295, 1.0], [61, 296, 1.0], [61, 297, 1.0], [61, 298, 1.0], [61, 299, 1.0], [62, 287, 1.0], [62, 288, 1.0], [62, 289, 1.0], [62, 290, 1.0], [62, 291, 1.0], [62, 292, 1.0], [62, 293, 1.0], [62, 294, 1.0], [62, 295, 1.0], [62, 296, 1.0], [62, 297, 1.0], [62, 298, 1.0], [62, 299, 1.0], [63, 287, 1.0], [63, 288, 1.0], [63, 289, 1.0], [63, 290, 1.0], [63, 291, 1.0], [63, 292, 1.0], [63, 293, 1.0], [63, 294, 1.0], [63, 295, 1.0], [63, 296, 1.0], [63, 297, 1.0], [63, 298, 1.0], [63, 299, 1.0], [64, 287, 1.0], [64, 288, 1.0], [64, 289, 1.0], [64, 290, 1.0], [64, 291, 1.0], [64, 292, 1.0], ...] |
| 517473341 | 517473341 | [[58, 272, 1.0], [58, 273, 1.0], [58, 274, 1.0], [58, 275, 1.0], [58, 276, 1.0], [58, 277, 1.0], [59, 271, 1.0], [59, 272, 1.0], [59, 273, 1.0], [59, 274, 1.0], [59, 275, 1.0], [59, 276, 1.0], [59, 277, 1.0], [59, 278, 1.0], [59, 279, 1.0], [59, 280, 1.0], [59, 281, 1.0], [59, 282, 1.0], [60, 271, 1.0], [60, 272, 1.0], [60, 273, 1.0], [60, 274, 1.0], [60, 275, 1.0], [60, 276, 1.0], [60, 277, 1.0], [60, 278, 1.0], [60, 279, 1.0], [60, 280, 1.0], [60, 281, 1.0], [60, 282, 1.0], [60, 283, 1.0], [61, 270, 1.0], [61, 271, 1.0], [61, 272, 1.0], [61, 273, 1.0], [61, 274, 1.0], [61, 275, 1.0], [61, 276, 1.0], [61, 277, 1.0], [61, 278, 1.0], [61, 279, 1.0], [61, 280, 1.0], [61, 281, 1.0], [61, 282, 1.0], [62, 270, 1.0], [62, 271, 1.0], [62, 272, 1.0], [62, 273, 1.0], [62, 274, 1.0], [62, 275, 1.0], [62, 276, 1.0], [62, 277, 1.0], [62, 278, 1.0], [62, 279, 1.0], [62, 280, 1.0], [62, 281, 1.0], [62, 282, 1.0], [63, 269, 1.0], [63, 270, 1.0], [63, 271, 1.0], [63, 272, 1.0], [63, 273, 1.0], [63, 274, 1.0], [63, 275, 1.0], [63, 276, 1.0], [63, 277, 1.0], [63, 278, 1.0], [63, 279, 1.0], [63, 280, 1.0], [63, 281, 1.0], [63, 282, 1.0], [64, 268, 1.0], [64, 269, 1.0], [64, 270, 1.0], [64, 271, 1.0], [64, 272, 1.0], [64, 273, 1.0], [64, 274, 1.0], [64, 275, 1.0], [64, 276, 1.0], [64, 277, 1.0], [64, 278, 1.0], [64, 279, 1.0], [64, 280, 1.0], [64, 281, 1.0], [64, 282, 1.0], [65, 268, 1.0], [65, 269, 1.0], [65, 270, 1.0], [65, 271, 1.0], [65, 272, 1.0], [65, 273, 1.0], [65, 274, 1.0], [65, 275, 1.0], [65, 276, 1.0], [65, 277, 1.0], [65, 278, 1.0], [65, 279, 1.0], [65, 280, 1.0], [65, 281, 1.0], ...] |
| 517473313 | 517473313 | [[33, 459, 1.0], [33, 460, 1.0], [33, 461, 1.0], [33, 462, 1.0], [33, 463, 1.0], [34, 458, 1.0], [34, 459, 1.0], [34, 460, 1.0], [34, 461, 1.0], [34, 462, 1.0], [34, 463, 1.0], [34, 464, 1.0], [35, 457, 1.0], [35, 458, 1.0], [35, 459, 1.0], [35, 460, 1.0], [35, 461, 1.0], [35, 462, 1.0], [35, 463, 1.0], [35, 464, 1.0], [35, 465, 1.0], [35, 466, 1.0], [36, 456, 1.0], [36, 457, 1.0], [36, 458, 1.0], [36, 459, 1.0], [36, 460, 1.0], [36, 461, 1.0], [36, 462, 1.0], [36, 463, 1.0], [36, 464, 1.0], [36, 465, 1.0], [36, 466, 1.0], [36, 467, 1.0], [37, 456, 1.0], [37, 457, 1.0], [37, 458, 1.0], [37, 459, 1.0], [37, 460, 1.0], [37, 461, 1.0], [37, 462, 1.0], [37, 463, 1.0], [37, 464, 1.0], [37, 465, 1.0], [37, 466, 1.0], [37, 467, 1.0], [38, 455, 1.0], [38, 456, 1.0], [38, 457, 1.0], [38, 458, 1.0], [38, 459, 1.0], [38, 460, 1.0], [38, 461, 1.0], [38, 462, 1.0], [38, 463, 1.0], [38, 464, 1.0], [38, 465, 1.0], [38, 466, 1.0], [38, 467, 1.0], [39, 455, 1.0], [39, 456, 1.0], [39, 457, 1.0], [39, 458, 1.0], [39, 459, 1.0], [39, 460, 1.0], [39, 461, 1.0], [39, 462, 1.0], [39, 463, 1.0], [39, 464, 1.0], [39, 465, 1.0], [39, 466, 1.0], [39, 467, 1.0], [40, 455, 1.0], [40, 456, 1.0], [40, 457, 1.0], [40, 458, 1.0], [40, 459, 1.0], [40, 460, 1.0], [40, 461, 1.0], [40, 462, 1.0], [40, 463, 1.0], [40, 464, 1.0], [40, 465, 1.0], [40, 466, 1.0], [41, 455, 1.0], [41, 456, 1.0], [41, 457, 1.0], [41, 458, 1.0], [41, 459, 1.0], [41, 460, 1.0], [41, 461, 1.0], [41, 462, 1.0], [41, 463, 1.0], [41, 464, 1.0], [41, 465, 1.0], [41, 466, 1.0], [42, 455, 1.0], [42, 456, 1.0], [42, 457, 1.0], [42, 458, 1.0], ...] |
| 517473255 | 517473255 | [[41, 493, 1.0], [41, 494, 1.0], [41, 495, 1.0], [41, 496, 1.0], [42, 492, 1.0], [42, 493, 1.0], [42, 494, 1.0], [42, 495, 1.0], [42, 496, 1.0], [42, 497, 1.0], [43, 489, 1.0], [43, 490, 1.0], [43, 491, 1.0], [43, 492, 1.0], [43, 493, 1.0], [43, 494, 1.0], [43, 495, 1.0], [43, 496, 1.0], [43, 497, 1.0], [43, 498, 1.0], [44, 488, 1.0], [44, 489, 1.0], [44, 490, 1.0], [44, 491, 1.0], [44, 492, 1.0], [44, 493, 1.0], [44, 494, 1.0], [44, 495, 1.0], [44, 496, 1.0], [44, 497, 1.0], [44, 498, 1.0], [45, 487, 1.0], [45, 488, 1.0], [45, 489, 1.0], [45, 490, 1.0], [45, 491, 1.0], [45, 492, 1.0], [45, 493, 1.0], [45, 494, 1.0], [45, 495, 1.0], [45, 496, 1.0], [45, 497, 1.0], [45, 498, 1.0], [46, 486, 1.0], [46, 487, 1.0], [46, 488, 1.0], [46, 489, 1.0], [46, 490, 1.0], [46, 491, 1.0], [46, 492, 1.0], [46, 493, 1.0], [46, 494, 1.0], [46, 495, 1.0], [46, 496, 1.0], [46, 497, 1.0], [46, 498, 1.0], [47, 486, 1.0], [47, 487, 1.0], [47, 488, 1.0], [47, 489, 1.0], [47, 490, 1.0], [47, 491, 1.0], [47, 492, 1.0], [47, 493, 1.0], [47, 494, 1.0], [47, 495, 1.0], [47, 496, 1.0], [47, 497, 1.0], [47, 498, 1.0], [47, 499, 1.0], [48, 486, 1.0], [48, 487, 1.0], [48, 488, 1.0], [48, 489, 1.0], [48, 490, 1.0], [48, 491, 1.0], [48, 492, 1.0], [48, 493, 1.0], [48, 494, 1.0], [48, 495, 1.0], [48, 496, 1.0], [48, 497, 1.0], [48, 498, 1.0], [48, 499, 1.0], [49, 486, 1.0], [49, 487, 1.0], [49, 488, 1.0], [49, 489, 1.0], [49, 490, 1.0], [49, 491, 1.0], [49, 492, 1.0], [49, 493, 1.0], [49, 494, 1.0], [49, 495, 1.0], [49, 496, 1.0], [49, 497, 1.0], [49, 498, 1.0], [49, 499, 1.0], [50, 486, 1.0], [50, 487, 1.0], ...] |
... and 170 more row(s).
DfOverFEvents
resolution: -1.0
comments: no comments
description: Events from the ΔF/F detected using the L0 method from the AllenSDK. Please consult the AllenSDK for more details of the calculation.
conversion: 1.0
offset: 0.0
unit: a.u.
data
| Data type | float64 |
|---|---|
| Shape | (113888, 174) |
| Array size | 151.19 MiB |
timestamps (link to processing/ophys/Fluorescence/Corrected/timestamps)
| Data type | float64 |
|---|---|
| Shape | (113888,) |
| Array size | 889.75 KiB |
timestamps_unit: seconds
interval: 1
rois
description: The regions of interest (ROIs) this response series refers to.
table
description: Segmented regions of interest (ROI).
imaging_plane
optical_channel
0
description: An optical channel used to collection light emission during two-photon calcium imaging.
emission_lambda: nan
description: The imaging plane sampled by the two-photon calcium imaging at a depth of {depth} µm.
device
description: A Nikon A1R-MP multiphoton microscope. This system was adapted to provide space to accommodate the behavior apparatus.
manufacturer: Nikon
excitation_lambda: 910.0
indicator: GCaMP6f
location: VISp
conversion: 1.0
unit: meters
origin_coords_unit: meters
grid_spacing
| Data type | float64 |
|---|---|
| Shape | (2,) |
| Array size | 16.00 bytes |
[0.78 0.78]
grid_spacing_unit: micrometers
table
| global_roi_id | pixel_mask | |
|---|---|---|
| id | ||
| 517473350 | 517473350 | [[55, 291, 1.0], [55, 292, 1.0], [56, 290, 1.0], [56, 291, 1.0], [56, 292, 1.0], [56, 293, 1.0], [56, 294, 1.0], [56, 295, 1.0], [56, 296, 1.0], [57, 289, 1.0], [57, 290, 1.0], [57, 291, 1.0], [57, 292, 1.0], [57, 293, 1.0], [57, 294, 1.0], [57, 295, 1.0], [57, 296, 1.0], [57, 297, 1.0], [57, 298, 1.0], [58, 288, 1.0], [58, 289, 1.0], [58, 290, 1.0], [58, 291, 1.0], [58, 292, 1.0], [58, 293, 1.0], [58, 294, 1.0], [58, 295, 1.0], [58, 296, 1.0], [58, 297, 1.0], [58, 298, 1.0], [58, 299, 1.0], [59, 288, 1.0], [59, 289, 1.0], [59, 290, 1.0], [59, 291, 1.0], [59, 292, 1.0], [59, 293, 1.0], [59, 294, 1.0], [59, 295, 1.0], [59, 296, 1.0], [59, 297, 1.0], [59, 298, 1.0], [59, 299, 1.0], [60, 288, 1.0], [60, 289, 1.0], [60, 290, 1.0], [60, 291, 1.0], [60, 292, 1.0], [60, 293, 1.0], [60, 294, 1.0], [60, 295, 1.0], [60, 296, 1.0], [60, 297, 1.0], [60, 298, 1.0], [60, 299, 1.0], [61, 287, 1.0], [61, 288, 1.0], [61, 289, 1.0], [61, 290, 1.0], [61, 291, 1.0], [61, 292, 1.0], [61, 293, 1.0], [61, 294, 1.0], [61, 295, 1.0], [61, 296, 1.0], [61, 297, 1.0], [61, 298, 1.0], [61, 299, 1.0], [62, 287, 1.0], [62, 288, 1.0], [62, 289, 1.0], [62, 290, 1.0], [62, 291, 1.0], [62, 292, 1.0], [62, 293, 1.0], [62, 294, 1.0], [62, 295, 1.0], [62, 296, 1.0], [62, 297, 1.0], [62, 298, 1.0], [62, 299, 1.0], [63, 287, 1.0], [63, 288, 1.0], [63, 289, 1.0], [63, 290, 1.0], [63, 291, 1.0], [63, 292, 1.0], [63, 293, 1.0], [63, 294, 1.0], [63, 295, 1.0], [63, 296, 1.0], [63, 297, 1.0], [63, 298, 1.0], [63, 299, 1.0], [64, 287, 1.0], [64, 288, 1.0], [64, 289, 1.0], [64, 290, 1.0], [64, 291, 1.0], [64, 292, 1.0], ...] |
| 517473341 | 517473341 | [[58, 272, 1.0], [58, 273, 1.0], [58, 274, 1.0], [58, 275, 1.0], [58, 276, 1.0], [58, 277, 1.0], [59, 271, 1.0], [59, 272, 1.0], [59, 273, 1.0], [59, 274, 1.0], [59, 275, 1.0], [59, 276, 1.0], [59, 277, 1.0], [59, 278, 1.0], [59, 279, 1.0], [59, 280, 1.0], [59, 281, 1.0], [59, 282, 1.0], [60, 271, 1.0], [60, 272, 1.0], [60, 273, 1.0], [60, 274, 1.0], [60, 275, 1.0], [60, 276, 1.0], [60, 277, 1.0], [60, 278, 1.0], [60, 279, 1.0], [60, 280, 1.0], [60, 281, 1.0], [60, 282, 1.0], [60, 283, 1.0], [61, 270, 1.0], [61, 271, 1.0], [61, 272, 1.0], [61, 273, 1.0], [61, 274, 1.0], [61, 275, 1.0], [61, 276, 1.0], [61, 277, 1.0], [61, 278, 1.0], [61, 279, 1.0], [61, 280, 1.0], [61, 281, 1.0], [61, 282, 1.0], [62, 270, 1.0], [62, 271, 1.0], [62, 272, 1.0], [62, 273, 1.0], [62, 274, 1.0], [62, 275, 1.0], [62, 276, 1.0], [62, 277, 1.0], [62, 278, 1.0], [62, 279, 1.0], [62, 280, 1.0], [62, 281, 1.0], [62, 282, 1.0], [63, 269, 1.0], [63, 270, 1.0], [63, 271, 1.0], [63, 272, 1.0], [63, 273, 1.0], [63, 274, 1.0], [63, 275, 1.0], [63, 276, 1.0], [63, 277, 1.0], [63, 278, 1.0], [63, 279, 1.0], [63, 280, 1.0], [63, 281, 1.0], [63, 282, 1.0], [64, 268, 1.0], [64, 269, 1.0], [64, 270, 1.0], [64, 271, 1.0], [64, 272, 1.0], [64, 273, 1.0], [64, 274, 1.0], [64, 275, 1.0], [64, 276, 1.0], [64, 277, 1.0], [64, 278, 1.0], [64, 279, 1.0], [64, 280, 1.0], [64, 281, 1.0], [64, 282, 1.0], [65, 268, 1.0], [65, 269, 1.0], [65, 270, 1.0], [65, 271, 1.0], [65, 272, 1.0], [65, 273, 1.0], [65, 274, 1.0], [65, 275, 1.0], [65, 276, 1.0], [65, 277, 1.0], [65, 278, 1.0], [65, 279, 1.0], [65, 280, 1.0], [65, 281, 1.0], ...] |
| 517473313 | 517473313 | [[33, 459, 1.0], [33, 460, 1.0], [33, 461, 1.0], [33, 462, 1.0], [33, 463, 1.0], [34, 458, 1.0], [34, 459, 1.0], [34, 460, 1.0], [34, 461, 1.0], [34, 462, 1.0], [34, 463, 1.0], [34, 464, 1.0], [35, 457, 1.0], [35, 458, 1.0], [35, 459, 1.0], [35, 460, 1.0], [35, 461, 1.0], [35, 462, 1.0], [35, 463, 1.0], [35, 464, 1.0], [35, 465, 1.0], [35, 466, 1.0], [36, 456, 1.0], [36, 457, 1.0], [36, 458, 1.0], [36, 459, 1.0], [36, 460, 1.0], [36, 461, 1.0], [36, 462, 1.0], [36, 463, 1.0], [36, 464, 1.0], [36, 465, 1.0], [36, 466, 1.0], [36, 467, 1.0], [37, 456, 1.0], [37, 457, 1.0], [37, 458, 1.0], [37, 459, 1.0], [37, 460, 1.0], [37, 461, 1.0], [37, 462, 1.0], [37, 463, 1.0], [37, 464, 1.0], [37, 465, 1.0], [37, 466, 1.0], [37, 467, 1.0], [38, 455, 1.0], [38, 456, 1.0], [38, 457, 1.0], [38, 458, 1.0], [38, 459, 1.0], [38, 460, 1.0], [38, 461, 1.0], [38, 462, 1.0], [38, 463, 1.0], [38, 464, 1.0], [38, 465, 1.0], [38, 466, 1.0], [38, 467, 1.0], [39, 455, 1.0], [39, 456, 1.0], [39, 457, 1.0], [39, 458, 1.0], [39, 459, 1.0], [39, 460, 1.0], [39, 461, 1.0], [39, 462, 1.0], [39, 463, 1.0], [39, 464, 1.0], [39, 465, 1.0], [39, 466, 1.0], [39, 467, 1.0], [40, 455, 1.0], [40, 456, 1.0], [40, 457, 1.0], [40, 458, 1.0], [40, 459, 1.0], [40, 460, 1.0], [40, 461, 1.0], [40, 462, 1.0], [40, 463, 1.0], [40, 464, 1.0], [40, 465, 1.0], [40, 466, 1.0], [41, 455, 1.0], [41, 456, 1.0], [41, 457, 1.0], [41, 458, 1.0], [41, 459, 1.0], [41, 460, 1.0], [41, 461, 1.0], [41, 462, 1.0], [41, 463, 1.0], [41, 464, 1.0], [41, 465, 1.0], [41, 466, 1.0], [42, 455, 1.0], [42, 456, 1.0], [42, 457, 1.0], [42, 458, 1.0], ...] |
| 517473255 | 517473255 | [[41, 493, 1.0], [41, 494, 1.0], [41, 495, 1.0], [41, 496, 1.0], [42, 492, 1.0], [42, 493, 1.0], [42, 494, 1.0], [42, 495, 1.0], [42, 496, 1.0], [42, 497, 1.0], [43, 489, 1.0], [43, 490, 1.0], [43, 491, 1.0], [43, 492, 1.0], [43, 493, 1.0], [43, 494, 1.0], [43, 495, 1.0], [43, 496, 1.0], [43, 497, 1.0], [43, 498, 1.0], [44, 488, 1.0], [44, 489, 1.0], [44, 490, 1.0], [44, 491, 1.0], [44, 492, 1.0], [44, 493, 1.0], [44, 494, 1.0], [44, 495, 1.0], [44, 496, 1.0], [44, 497, 1.0], [44, 498, 1.0], [45, 487, 1.0], [45, 488, 1.0], [45, 489, 1.0], [45, 490, 1.0], [45, 491, 1.0], [45, 492, 1.0], [45, 493, 1.0], [45, 494, 1.0], [45, 495, 1.0], [45, 496, 1.0], [45, 497, 1.0], [45, 498, 1.0], [46, 486, 1.0], [46, 487, 1.0], [46, 488, 1.0], [46, 489, 1.0], [46, 490, 1.0], [46, 491, 1.0], [46, 492, 1.0], [46, 493, 1.0], [46, 494, 1.0], [46, 495, 1.0], [46, 496, 1.0], [46, 497, 1.0], [46, 498, 1.0], [47, 486, 1.0], [47, 487, 1.0], [47, 488, 1.0], [47, 489, 1.0], [47, 490, 1.0], [47, 491, 1.0], [47, 492, 1.0], [47, 493, 1.0], [47, 494, 1.0], [47, 495, 1.0], [47, 496, 1.0], [47, 497, 1.0], [47, 498, 1.0], [47, 499, 1.0], [48, 486, 1.0], [48, 487, 1.0], [48, 488, 1.0], [48, 489, 1.0], [48, 490, 1.0], [48, 491, 1.0], [48, 492, 1.0], [48, 493, 1.0], [48, 494, 1.0], [48, 495, 1.0], [48, 496, 1.0], [48, 497, 1.0], [48, 498, 1.0], [48, 499, 1.0], [49, 486, 1.0], [49, 487, 1.0], [49, 488, 1.0], [49, 489, 1.0], [49, 490, 1.0], [49, 491, 1.0], [49, 492, 1.0], [49, 493, 1.0], [49, 494, 1.0], [49, 495, 1.0], [49, 496, 1.0], [49, 497, 1.0], [49, 498, 1.0], [49, 499, 1.0], [50, 486, 1.0], [50, 487, 1.0], ...] |
... and 170 more row(s).
Fluorescence
roi_response_series
Corrected
resolution: -1.0
comments: no comments
description: Fluorescence per region of interest (ROI) from the raw imaging after spatial demixing and subtraction of neuropil background, but prior to dF/F normalization.
conversion: 1.0
offset: 0.0
unit: n.a.
data
| Data type | float32 |
|---|---|
| Shape | (113888, 174) |
| Array size | 75.59 MiB |
timestamps
| Data type | float64 |
|---|---|
| Shape | (113888,) |
| Array size | 889.75 KiB |
timestamps_unit: seconds
interval: 1
rois
description: The regions of interest (ROIs) this response series refers to.
table
description: Segmented regions of interest (ROI).
imaging_plane
optical_channel
0
description: An optical channel used to collection light emission during two-photon calcium imaging.
emission_lambda: nan
description: The imaging plane sampled by the two-photon calcium imaging at a depth of {depth} µm.
device
description: A Nikon A1R-MP multiphoton microscope. This system was adapted to provide space to accommodate the behavior apparatus.
manufacturer: Nikon
excitation_lambda: 910.0
indicator: GCaMP6f
location: VISp
conversion: 1.0
unit: meters
origin_coords_unit: meters
grid_spacing
| Data type | float64 |
|---|---|
| Shape | (2,) |
| Array size | 16.00 bytes |
[0.78 0.78]
grid_spacing_unit: micrometers
table
| global_roi_id | pixel_mask | |
|---|---|---|
| id | ||
| 517473350 | 517473350 | [[55, 291, 1.0], [55, 292, 1.0], [56, 290, 1.0], [56, 291, 1.0], [56, 292, 1.0], [56, 293, 1.0], [56, 294, 1.0], [56, 295, 1.0], [56, 296, 1.0], [57, 289, 1.0], [57, 290, 1.0], [57, 291, 1.0], [57, 292, 1.0], [57, 293, 1.0], [57, 294, 1.0], [57, 295, 1.0], [57, 296, 1.0], [57, 297, 1.0], [57, 298, 1.0], [58, 288, 1.0], [58, 289, 1.0], [58, 290, 1.0], [58, 291, 1.0], [58, 292, 1.0], [58, 293, 1.0], [58, 294, 1.0], [58, 295, 1.0], [58, 296, 1.0], [58, 297, 1.0], [58, 298, 1.0], [58, 299, 1.0], [59, 288, 1.0], [59, 289, 1.0], [59, 290, 1.0], [59, 291, 1.0], [59, 292, 1.0], [59, 293, 1.0], [59, 294, 1.0], [59, 295, 1.0], [59, 296, 1.0], [59, 297, 1.0], [59, 298, 1.0], [59, 299, 1.0], [60, 288, 1.0], [60, 289, 1.0], [60, 290, 1.0], [60, 291, 1.0], [60, 292, 1.0], [60, 293, 1.0], [60, 294, 1.0], [60, 295, 1.0], [60, 296, 1.0], [60, 297, 1.0], [60, 298, 1.0], [60, 299, 1.0], [61, 287, 1.0], [61, 288, 1.0], [61, 289, 1.0], [61, 290, 1.0], [61, 291, 1.0], [61, 292, 1.0], [61, 293, 1.0], [61, 294, 1.0], [61, 295, 1.0], [61, 296, 1.0], [61, 297, 1.0], [61, 298, 1.0], [61, 299, 1.0], [62, 287, 1.0], [62, 288, 1.0], [62, 289, 1.0], [62, 290, 1.0], [62, 291, 1.0], [62, 292, 1.0], [62, 293, 1.0], [62, 294, 1.0], [62, 295, 1.0], [62, 296, 1.0], [62, 297, 1.0], [62, 298, 1.0], [62, 299, 1.0], [63, 287, 1.0], [63, 288, 1.0], [63, 289, 1.0], [63, 290, 1.0], [63, 291, 1.0], [63, 292, 1.0], [63, 293, 1.0], [63, 294, 1.0], [63, 295, 1.0], [63, 296, 1.0], [63, 297, 1.0], [63, 298, 1.0], [63, 299, 1.0], [64, 287, 1.0], [64, 288, 1.0], [64, 289, 1.0], [64, 290, 1.0], [64, 291, 1.0], [64, 292, 1.0], ...] |
| 517473341 | 517473341 | [[58, 272, 1.0], [58, 273, 1.0], [58, 274, 1.0], [58, 275, 1.0], [58, 276, 1.0], [58, 277, 1.0], [59, 271, 1.0], [59, 272, 1.0], [59, 273, 1.0], [59, 274, 1.0], [59, 275, 1.0], [59, 276, 1.0], [59, 277, 1.0], [59, 278, 1.0], [59, 279, 1.0], [59, 280, 1.0], [59, 281, 1.0], [59, 282, 1.0], [60, 271, 1.0], [60, 272, 1.0], [60, 273, 1.0], [60, 274, 1.0], [60, 275, 1.0], [60, 276, 1.0], [60, 277, 1.0], [60, 278, 1.0], [60, 279, 1.0], [60, 280, 1.0], [60, 281, 1.0], [60, 282, 1.0], [60, 283, 1.0], [61, 270, 1.0], [61, 271, 1.0], [61, 272, 1.0], [61, 273, 1.0], [61, 274, 1.0], [61, 275, 1.0], [61, 276, 1.0], [61, 277, 1.0], [61, 278, 1.0], [61, 279, 1.0], [61, 280, 1.0], [61, 281, 1.0], [61, 282, 1.0], [62, 270, 1.0], [62, 271, 1.0], [62, 272, 1.0], [62, 273, 1.0], [62, 274, 1.0], [62, 275, 1.0], [62, 276, 1.0], [62, 277, 1.0], [62, 278, 1.0], [62, 279, 1.0], [62, 280, 1.0], [62, 281, 1.0], [62, 282, 1.0], [63, 269, 1.0], [63, 270, 1.0], [63, 271, 1.0], [63, 272, 1.0], [63, 273, 1.0], [63, 274, 1.0], [63, 275, 1.0], [63, 276, 1.0], [63, 277, 1.0], [63, 278, 1.0], [63, 279, 1.0], [63, 280, 1.0], [63, 281, 1.0], [63, 282, 1.0], [64, 268, 1.0], [64, 269, 1.0], [64, 270, 1.0], [64, 271, 1.0], [64, 272, 1.0], [64, 273, 1.0], [64, 274, 1.0], [64, 275, 1.0], [64, 276, 1.0], [64, 277, 1.0], [64, 278, 1.0], [64, 279, 1.0], [64, 280, 1.0], [64, 281, 1.0], [64, 282, 1.0], [65, 268, 1.0], [65, 269, 1.0], [65, 270, 1.0], [65, 271, 1.0], [65, 272, 1.0], [65, 273, 1.0], [65, 274, 1.0], [65, 275, 1.0], [65, 276, 1.0], [65, 277, 1.0], [65, 278, 1.0], [65, 279, 1.0], [65, 280, 1.0], [65, 281, 1.0], ...] |
| 517473313 | 517473313 | [[33, 459, 1.0], [33, 460, 1.0], [33, 461, 1.0], [33, 462, 1.0], [33, 463, 1.0], [34, 458, 1.0], [34, 459, 1.0], [34, 460, 1.0], [34, 461, 1.0], [34, 462, 1.0], [34, 463, 1.0], [34, 464, 1.0], [35, 457, 1.0], [35, 458, 1.0], [35, 459, 1.0], [35, 460, 1.0], [35, 461, 1.0], [35, 462, 1.0], [35, 463, 1.0], [35, 464, 1.0], [35, 465, 1.0], [35, 466, 1.0], [36, 456, 1.0], [36, 457, 1.0], [36, 458, 1.0], [36, 459, 1.0], [36, 460, 1.0], [36, 461, 1.0], [36, 462, 1.0], [36, 463, 1.0], [36, 464, 1.0], [36, 465, 1.0], [36, 466, 1.0], [36, 467, 1.0], [37, 456, 1.0], [37, 457, 1.0], [37, 458, 1.0], [37, 459, 1.0], [37, 460, 1.0], [37, 461, 1.0], [37, 462, 1.0], [37, 463, 1.0], [37, 464, 1.0], [37, 465, 1.0], [37, 466, 1.0], [37, 467, 1.0], [38, 455, 1.0], [38, 456, 1.0], [38, 457, 1.0], [38, 458, 1.0], [38, 459, 1.0], [38, 460, 1.0], [38, 461, 1.0], [38, 462, 1.0], [38, 463, 1.0], [38, 464, 1.0], [38, 465, 1.0], [38, 466, 1.0], [38, 467, 1.0], [39, 455, 1.0], [39, 456, 1.0], [39, 457, 1.0], [39, 458, 1.0], [39, 459, 1.0], [39, 460, 1.0], [39, 461, 1.0], [39, 462, 1.0], [39, 463, 1.0], [39, 464, 1.0], [39, 465, 1.0], [39, 466, 1.0], [39, 467, 1.0], [40, 455, 1.0], [40, 456, 1.0], [40, 457, 1.0], [40, 458, 1.0], [40, 459, 1.0], [40, 460, 1.0], [40, 461, 1.0], [40, 462, 1.0], [40, 463, 1.0], [40, 464, 1.0], [40, 465, 1.0], [40, 466, 1.0], [41, 455, 1.0], [41, 456, 1.0], [41, 457, 1.0], [41, 458, 1.0], [41, 459, 1.0], [41, 460, 1.0], [41, 461, 1.0], [41, 462, 1.0], [41, 463, 1.0], [41, 464, 1.0], [41, 465, 1.0], [41, 466, 1.0], [42, 455, 1.0], [42, 456, 1.0], [42, 457, 1.0], [42, 458, 1.0], ...] |
| 517473255 | 517473255 | [[41, 493, 1.0], [41, 494, 1.0], [41, 495, 1.0], [41, 496, 1.0], [42, 492, 1.0], [42, 493, 1.0], [42, 494, 1.0], [42, 495, 1.0], [42, 496, 1.0], [42, 497, 1.0], [43, 489, 1.0], [43, 490, 1.0], [43, 491, 1.0], [43, 492, 1.0], [43, 493, 1.0], [43, 494, 1.0], [43, 495, 1.0], [43, 496, 1.0], [43, 497, 1.0], [43, 498, 1.0], [44, 488, 1.0], [44, 489, 1.0], [44, 490, 1.0], [44, 491, 1.0], [44, 492, 1.0], [44, 493, 1.0], [44, 494, 1.0], [44, 495, 1.0], [44, 496, 1.0], [44, 497, 1.0], [44, 498, 1.0], [45, 487, 1.0], [45, 488, 1.0], [45, 489, 1.0], [45, 490, 1.0], [45, 491, 1.0], [45, 492, 1.0], [45, 493, 1.0], [45, 494, 1.0], [45, 495, 1.0], [45, 496, 1.0], [45, 497, 1.0], [45, 498, 1.0], [46, 486, 1.0], [46, 487, 1.0], [46, 488, 1.0], [46, 489, 1.0], [46, 490, 1.0], [46, 491, 1.0], [46, 492, 1.0], [46, 493, 1.0], [46, 494, 1.0], [46, 495, 1.0], [46, 496, 1.0], [46, 497, 1.0], [46, 498, 1.0], [47, 486, 1.0], [47, 487, 1.0], [47, 488, 1.0], [47, 489, 1.0], [47, 490, 1.0], [47, 491, 1.0], [47, 492, 1.0], [47, 493, 1.0], [47, 494, 1.0], [47, 495, 1.0], [47, 496, 1.0], [47, 497, 1.0], [47, 498, 1.0], [47, 499, 1.0], [48, 486, 1.0], [48, 487, 1.0], [48, 488, 1.0], [48, 489, 1.0], [48, 490, 1.0], [48, 491, 1.0], [48, 492, 1.0], [48, 493, 1.0], [48, 494, 1.0], [48, 495, 1.0], [48, 496, 1.0], [48, 497, 1.0], [48, 498, 1.0], [48, 499, 1.0], [49, 486, 1.0], [49, 487, 1.0], [49, 488, 1.0], [49, 489, 1.0], [49, 490, 1.0], [49, 491, 1.0], [49, 492, 1.0], [49, 493, 1.0], [49, 494, 1.0], [49, 495, 1.0], [49, 496, 1.0], [49, 497, 1.0], [49, 498, 1.0], [49, 499, 1.0], [50, 486, 1.0], [50, 487, 1.0], ...] |
... and 170 more row(s).
timestamp_link
0: processing/ophys/DfOverF/DfOverF/timestamps
1: processing/ophys/DfOverF/DfOverFEvents/timestamps
2: processing/ophys/Fluorescence/Demixed/timestamps
3: processing/ophys/Fluorescence/Neuropil/timestamps
Demixed
resolution: -1.0
comments: no comments
description: Spatially demixed traces of potentially overlapping masks.
conversion: 1.0
offset: 0.0
unit: n.a.
data
| Data type | float32 |
|---|---|
| Shape | (113888, 174) |
| Array size | 75.59 MiB |
timestamps (link to processing/ophys/Fluorescence/Corrected/timestamps)
| Data type | float64 |
|---|---|
| Shape | (113888,) |
| Array size | 889.75 KiB |
timestamps_unit: seconds
interval: 1
rois
description: The regions of interest (ROIs) this response series refers to.
table
description: Segmented regions of interest (ROI).
imaging_plane
optical_channel
0
description: An optical channel used to collection light emission during two-photon calcium imaging.
emission_lambda: nan
description: The imaging plane sampled by the two-photon calcium imaging at a depth of {depth} µm.
device
description: A Nikon A1R-MP multiphoton microscope. This system was adapted to provide space to accommodate the behavior apparatus.
manufacturer: Nikon
excitation_lambda: 910.0
indicator: GCaMP6f
location: VISp
conversion: 1.0
unit: meters
origin_coords_unit: meters
grid_spacing
| Data type | float64 |
|---|---|
| Shape | (2,) |
| Array size | 16.00 bytes |
[0.78 0.78]
grid_spacing_unit: micrometers
table
| global_roi_id | pixel_mask | |
|---|---|---|
| id | ||
| 517473350 | 517473350 | [[55, 291, 1.0], [55, 292, 1.0], [56, 290, 1.0], [56, 291, 1.0], [56, 292, 1.0], [56, 293, 1.0], [56, 294, 1.0], [56, 295, 1.0], [56, 296, 1.0], [57, 289, 1.0], [57, 290, 1.0], [57, 291, 1.0], [57, 292, 1.0], [57, 293, 1.0], [57, 294, 1.0], [57, 295, 1.0], [57, 296, 1.0], [57, 297, 1.0], [57, 298, 1.0], [58, 288, 1.0], [58, 289, 1.0], [58, 290, 1.0], [58, 291, 1.0], [58, 292, 1.0], [58, 293, 1.0], [58, 294, 1.0], [58, 295, 1.0], [58, 296, 1.0], [58, 297, 1.0], [58, 298, 1.0], [58, 299, 1.0], [59, 288, 1.0], [59, 289, 1.0], [59, 290, 1.0], [59, 291, 1.0], [59, 292, 1.0], [59, 293, 1.0], [59, 294, 1.0], [59, 295, 1.0], [59, 296, 1.0], [59, 297, 1.0], [59, 298, 1.0], [59, 299, 1.0], [60, 288, 1.0], [60, 289, 1.0], [60, 290, 1.0], [60, 291, 1.0], [60, 292, 1.0], [60, 293, 1.0], [60, 294, 1.0], [60, 295, 1.0], [60, 296, 1.0], [60, 297, 1.0], [60, 298, 1.0], [60, 299, 1.0], [61, 287, 1.0], [61, 288, 1.0], [61, 289, 1.0], [61, 290, 1.0], [61, 291, 1.0], [61, 292, 1.0], [61, 293, 1.0], [61, 294, 1.0], [61, 295, 1.0], [61, 296, 1.0], [61, 297, 1.0], [61, 298, 1.0], [61, 299, 1.0], [62, 287, 1.0], [62, 288, 1.0], [62, 289, 1.0], [62, 290, 1.0], [62, 291, 1.0], [62, 292, 1.0], [62, 293, 1.0], [62, 294, 1.0], [62, 295, 1.0], [62, 296, 1.0], [62, 297, 1.0], [62, 298, 1.0], [62, 299, 1.0], [63, 287, 1.0], [63, 288, 1.0], [63, 289, 1.0], [63, 290, 1.0], [63, 291, 1.0], [63, 292, 1.0], [63, 293, 1.0], [63, 294, 1.0], [63, 295, 1.0], [63, 296, 1.0], [63, 297, 1.0], [63, 298, 1.0], [63, 299, 1.0], [64, 287, 1.0], [64, 288, 1.0], [64, 289, 1.0], [64, 290, 1.0], [64, 291, 1.0], [64, 292, 1.0], ...] |
| 517473341 | 517473341 | [[58, 272, 1.0], [58, 273, 1.0], [58, 274, 1.0], [58, 275, 1.0], [58, 276, 1.0], [58, 277, 1.0], [59, 271, 1.0], [59, 272, 1.0], [59, 273, 1.0], [59, 274, 1.0], [59, 275, 1.0], [59, 276, 1.0], [59, 277, 1.0], [59, 278, 1.0], [59, 279, 1.0], [59, 280, 1.0], [59, 281, 1.0], [59, 282, 1.0], [60, 271, 1.0], [60, 272, 1.0], [60, 273, 1.0], [60, 274, 1.0], [60, 275, 1.0], [60, 276, 1.0], [60, 277, 1.0], [60, 278, 1.0], [60, 279, 1.0], [60, 280, 1.0], [60, 281, 1.0], [60, 282, 1.0], [60, 283, 1.0], [61, 270, 1.0], [61, 271, 1.0], [61, 272, 1.0], [61, 273, 1.0], [61, 274, 1.0], [61, 275, 1.0], [61, 276, 1.0], [61, 277, 1.0], [61, 278, 1.0], [61, 279, 1.0], [61, 280, 1.0], [61, 281, 1.0], [61, 282, 1.0], [62, 270, 1.0], [62, 271, 1.0], [62, 272, 1.0], [62, 273, 1.0], [62, 274, 1.0], [62, 275, 1.0], [62, 276, 1.0], [62, 277, 1.0], [62, 278, 1.0], [62, 279, 1.0], [62, 280, 1.0], [62, 281, 1.0], [62, 282, 1.0], [63, 269, 1.0], [63, 270, 1.0], [63, 271, 1.0], [63, 272, 1.0], [63, 273, 1.0], [63, 274, 1.0], [63, 275, 1.0], [63, 276, 1.0], [63, 277, 1.0], [63, 278, 1.0], [63, 279, 1.0], [63, 280, 1.0], [63, 281, 1.0], [63, 282, 1.0], [64, 268, 1.0], [64, 269, 1.0], [64, 270, 1.0], [64, 271, 1.0], [64, 272, 1.0], [64, 273, 1.0], [64, 274, 1.0], [64, 275, 1.0], [64, 276, 1.0], [64, 277, 1.0], [64, 278, 1.0], [64, 279, 1.0], [64, 280, 1.0], [64, 281, 1.0], [64, 282, 1.0], [65, 268, 1.0], [65, 269, 1.0], [65, 270, 1.0], [65, 271, 1.0], [65, 272, 1.0], [65, 273, 1.0], [65, 274, 1.0], [65, 275, 1.0], [65, 276, 1.0], [65, 277, 1.0], [65, 278, 1.0], [65, 279, 1.0], [65, 280, 1.0], [65, 281, 1.0], ...] |
| 517473313 | 517473313 | [[33, 459, 1.0], [33, 460, 1.0], [33, 461, 1.0], [33, 462, 1.0], [33, 463, 1.0], [34, 458, 1.0], [34, 459, 1.0], [34, 460, 1.0], [34, 461, 1.0], [34, 462, 1.0], [34, 463, 1.0], [34, 464, 1.0], [35, 457, 1.0], [35, 458, 1.0], [35, 459, 1.0], [35, 460, 1.0], [35, 461, 1.0], [35, 462, 1.0], [35, 463, 1.0], [35, 464, 1.0], [35, 465, 1.0], [35, 466, 1.0], [36, 456, 1.0], [36, 457, 1.0], [36, 458, 1.0], [36, 459, 1.0], [36, 460, 1.0], [36, 461, 1.0], [36, 462, 1.0], [36, 463, 1.0], [36, 464, 1.0], [36, 465, 1.0], [36, 466, 1.0], [36, 467, 1.0], [37, 456, 1.0], [37, 457, 1.0], [37, 458, 1.0], [37, 459, 1.0], [37, 460, 1.0], [37, 461, 1.0], [37, 462, 1.0], [37, 463, 1.0], [37, 464, 1.0], [37, 465, 1.0], [37, 466, 1.0], [37, 467, 1.0], [38, 455, 1.0], [38, 456, 1.0], [38, 457, 1.0], [38, 458, 1.0], [38, 459, 1.0], [38, 460, 1.0], [38, 461, 1.0], [38, 462, 1.0], [38, 463, 1.0], [38, 464, 1.0], [38, 465, 1.0], [38, 466, 1.0], [38, 467, 1.0], [39, 455, 1.0], [39, 456, 1.0], [39, 457, 1.0], [39, 458, 1.0], [39, 459, 1.0], [39, 460, 1.0], [39, 461, 1.0], [39, 462, 1.0], [39, 463, 1.0], [39, 464, 1.0], [39, 465, 1.0], [39, 466, 1.0], [39, 467, 1.0], [40, 455, 1.0], [40, 456, 1.0], [40, 457, 1.0], [40, 458, 1.0], [40, 459, 1.0], [40, 460, 1.0], [40, 461, 1.0], [40, 462, 1.0], [40, 463, 1.0], [40, 464, 1.0], [40, 465, 1.0], [40, 466, 1.0], [41, 455, 1.0], [41, 456, 1.0], [41, 457, 1.0], [41, 458, 1.0], [41, 459, 1.0], [41, 460, 1.0], [41, 461, 1.0], [41, 462, 1.0], [41, 463, 1.0], [41, 464, 1.0], [41, 465, 1.0], [41, 466, 1.0], [42, 455, 1.0], [42, 456, 1.0], [42, 457, 1.0], [42, 458, 1.0], ...] |
| 517473255 | 517473255 | [[41, 493, 1.0], [41, 494, 1.0], [41, 495, 1.0], [41, 496, 1.0], [42, 492, 1.0], [42, 493, 1.0], [42, 494, 1.0], [42, 495, 1.0], [42, 496, 1.0], [42, 497, 1.0], [43, 489, 1.0], [43, 490, 1.0], [43, 491, 1.0], [43, 492, 1.0], [43, 493, 1.0], [43, 494, 1.0], [43, 495, 1.0], [43, 496, 1.0], [43, 497, 1.0], [43, 498, 1.0], [44, 488, 1.0], [44, 489, 1.0], [44, 490, 1.0], [44, 491, 1.0], [44, 492, 1.0], [44, 493, 1.0], [44, 494, 1.0], [44, 495, 1.0], [44, 496, 1.0], [44, 497, 1.0], [44, 498, 1.0], [45, 487, 1.0], [45, 488, 1.0], [45, 489, 1.0], [45, 490, 1.0], [45, 491, 1.0], [45, 492, 1.0], [45, 493, 1.0], [45, 494, 1.0], [45, 495, 1.0], [45, 496, 1.0], [45, 497, 1.0], [45, 498, 1.0], [46, 486, 1.0], [46, 487, 1.0], [46, 488, 1.0], [46, 489, 1.0], [46, 490, 1.0], [46, 491, 1.0], [46, 492, 1.0], [46, 493, 1.0], [46, 494, 1.0], [46, 495, 1.0], [46, 496, 1.0], [46, 497, 1.0], [46, 498, 1.0], [47, 486, 1.0], [47, 487, 1.0], [47, 488, 1.0], [47, 489, 1.0], [47, 490, 1.0], [47, 491, 1.0], [47, 492, 1.0], [47, 493, 1.0], [47, 494, 1.0], [47, 495, 1.0], [47, 496, 1.0], [47, 497, 1.0], [47, 498, 1.0], [47, 499, 1.0], [48, 486, 1.0], [48, 487, 1.0], [48, 488, 1.0], [48, 489, 1.0], [48, 490, 1.0], [48, 491, 1.0], [48, 492, 1.0], [48, 493, 1.0], [48, 494, 1.0], [48, 495, 1.0], [48, 496, 1.0], [48, 497, 1.0], [48, 498, 1.0], [48, 499, 1.0], [49, 486, 1.0], [49, 487, 1.0], [49, 488, 1.0], [49, 489, 1.0], [49, 490, 1.0], [49, 491, 1.0], [49, 492, 1.0], [49, 493, 1.0], [49, 494, 1.0], [49, 495, 1.0], [49, 496, 1.0], [49, 497, 1.0], [49, 498, 1.0], [49, 499, 1.0], [50, 486, 1.0], [50, 487, 1.0], ...] |
... and 170 more row(s).
Neuropil
resolution: -1.0
comments: no comments
description: Fluorescence contaminated by background neuropil.
conversion: 1.0
offset: 0.0
unit: n.a.
data
| Data type | float32 |
|---|---|
| Shape | (113888, 174) |
| Array size | 75.59 MiB |
timestamps (link to processing/ophys/Fluorescence/Corrected/timestamps)
| Data type | float64 |
|---|---|
| Shape | (113888,) |
| Array size | 889.75 KiB |
timestamps_unit: seconds
interval: 1
rois
description: The regions of interest (ROIs) this response series refers to.
table
description: Segmented regions of interest (ROI).
imaging_plane
optical_channel
0
description: An optical channel used to collection light emission during two-photon calcium imaging.
emission_lambda: nan
description: The imaging plane sampled by the two-photon calcium imaging at a depth of {depth} µm.
device
description: A Nikon A1R-MP multiphoton microscope. This system was adapted to provide space to accommodate the behavior apparatus.
manufacturer: Nikon
excitation_lambda: 910.0
indicator: GCaMP6f
location: VISp
conversion: 1.0
unit: meters
origin_coords_unit: meters
grid_spacing
| Data type | float64 |
|---|---|
| Shape | (2,) |
| Array size | 16.00 bytes |
[0.78 0.78]
grid_spacing_unit: micrometers
table
| global_roi_id | pixel_mask | |
|---|---|---|
| id | ||
| 517473350 | 517473350 | [[55, 291, 1.0], [55, 292, 1.0], [56, 290, 1.0], [56, 291, 1.0], [56, 292, 1.0], [56, 293, 1.0], [56, 294, 1.0], [56, 295, 1.0], [56, 296, 1.0], [57, 289, 1.0], [57, 290, 1.0], [57, 291, 1.0], [57, 292, 1.0], [57, 293, 1.0], [57, 294, 1.0], [57, 295, 1.0], [57, 296, 1.0], [57, 297, 1.0], [57, 298, 1.0], [58, 288, 1.0], [58, 289, 1.0], [58, 290, 1.0], [58, 291, 1.0], [58, 292, 1.0], [58, 293, 1.0], [58, 294, 1.0], [58, 295, 1.0], [58, 296, 1.0], [58, 297, 1.0], [58, 298, 1.0], [58, 299, 1.0], [59, 288, 1.0], [59, 289, 1.0], [59, 290, 1.0], [59, 291, 1.0], [59, 292, 1.0], [59, 293, 1.0], [59, 294, 1.0], [59, 295, 1.0], [59, 296, 1.0], [59, 297, 1.0], [59, 298, 1.0], [59, 299, 1.0], [60, 288, 1.0], [60, 289, 1.0], [60, 290, 1.0], [60, 291, 1.0], [60, 292, 1.0], [60, 293, 1.0], [60, 294, 1.0], [60, 295, 1.0], [60, 296, 1.0], [60, 297, 1.0], [60, 298, 1.0], [60, 299, 1.0], [61, 287, 1.0], [61, 288, 1.0], [61, 289, 1.0], [61, 290, 1.0], [61, 291, 1.0], [61, 292, 1.0], [61, 293, 1.0], [61, 294, 1.0], [61, 295, 1.0], [61, 296, 1.0], [61, 297, 1.0], [61, 298, 1.0], [61, 299, 1.0], [62, 287, 1.0], [62, 288, 1.0], [62, 289, 1.0], [62, 290, 1.0], [62, 291, 1.0], [62, 292, 1.0], [62, 293, 1.0], [62, 294, 1.0], [62, 295, 1.0], [62, 296, 1.0], [62, 297, 1.0], [62, 298, 1.0], [62, 299, 1.0], [63, 287, 1.0], [63, 288, 1.0], [63, 289, 1.0], [63, 290, 1.0], [63, 291, 1.0], [63, 292, 1.0], [63, 293, 1.0], [63, 294, 1.0], [63, 295, 1.0], [63, 296, 1.0], [63, 297, 1.0], [63, 298, 1.0], [63, 299, 1.0], [64, 287, 1.0], [64, 288, 1.0], [64, 289, 1.0], [64, 290, 1.0], [64, 291, 1.0], [64, 292, 1.0], ...] |
| 517473341 | 517473341 | [[58, 272, 1.0], [58, 273, 1.0], [58, 274, 1.0], [58, 275, 1.0], [58, 276, 1.0], [58, 277, 1.0], [59, 271, 1.0], [59, 272, 1.0], [59, 273, 1.0], [59, 274, 1.0], [59, 275, 1.0], [59, 276, 1.0], [59, 277, 1.0], [59, 278, 1.0], [59, 279, 1.0], [59, 280, 1.0], [59, 281, 1.0], [59, 282, 1.0], [60, 271, 1.0], [60, 272, 1.0], [60, 273, 1.0], [60, 274, 1.0], [60, 275, 1.0], [60, 276, 1.0], [60, 277, 1.0], [60, 278, 1.0], [60, 279, 1.0], [60, 280, 1.0], [60, 281, 1.0], [60, 282, 1.0], [60, 283, 1.0], [61, 270, 1.0], [61, 271, 1.0], [61, 272, 1.0], [61, 273, 1.0], [61, 274, 1.0], [61, 275, 1.0], [61, 276, 1.0], [61, 277, 1.0], [61, 278, 1.0], [61, 279, 1.0], [61, 280, 1.0], [61, 281, 1.0], [61, 282, 1.0], [62, 270, 1.0], [62, 271, 1.0], [62, 272, 1.0], [62, 273, 1.0], [62, 274, 1.0], [62, 275, 1.0], [62, 276, 1.0], [62, 277, 1.0], [62, 278, 1.0], [62, 279, 1.0], [62, 280, 1.0], [62, 281, 1.0], [62, 282, 1.0], [63, 269, 1.0], [63, 270, 1.0], [63, 271, 1.0], [63, 272, 1.0], [63, 273, 1.0], [63, 274, 1.0], [63, 275, 1.0], [63, 276, 1.0], [63, 277, 1.0], [63, 278, 1.0], [63, 279, 1.0], [63, 280, 1.0], [63, 281, 1.0], [63, 282, 1.0], [64, 268, 1.0], [64, 269, 1.0], [64, 270, 1.0], [64, 271, 1.0], [64, 272, 1.0], [64, 273, 1.0], [64, 274, 1.0], [64, 275, 1.0], [64, 276, 1.0], [64, 277, 1.0], [64, 278, 1.0], [64, 279, 1.0], [64, 280, 1.0], [64, 281, 1.0], [64, 282, 1.0], [65, 268, 1.0], [65, 269, 1.0], [65, 270, 1.0], [65, 271, 1.0], [65, 272, 1.0], [65, 273, 1.0], [65, 274, 1.0], [65, 275, 1.0], [65, 276, 1.0], [65, 277, 1.0], [65, 278, 1.0], [65, 279, 1.0], [65, 280, 1.0], [65, 281, 1.0], ...] |
| 517473313 | 517473313 | [[33, 459, 1.0], [33, 460, 1.0], [33, 461, 1.0], [33, 462, 1.0], [33, 463, 1.0], [34, 458, 1.0], [34, 459, 1.0], [34, 460, 1.0], [34, 461, 1.0], [34, 462, 1.0], [34, 463, 1.0], [34, 464, 1.0], [35, 457, 1.0], [35, 458, 1.0], [35, 459, 1.0], [35, 460, 1.0], [35, 461, 1.0], [35, 462, 1.0], [35, 463, 1.0], [35, 464, 1.0], [35, 465, 1.0], [35, 466, 1.0], [36, 456, 1.0], [36, 457, 1.0], [36, 458, 1.0], [36, 459, 1.0], [36, 460, 1.0], [36, 461, 1.0], [36, 462, 1.0], [36, 463, 1.0], [36, 464, 1.0], [36, 465, 1.0], [36, 466, 1.0], [36, 467, 1.0], [37, 456, 1.0], [37, 457, 1.0], [37, 458, 1.0], [37, 459, 1.0], [37, 460, 1.0], [37, 461, 1.0], [37, 462, 1.0], [37, 463, 1.0], [37, 464, 1.0], [37, 465, 1.0], [37, 466, 1.0], [37, 467, 1.0], [38, 455, 1.0], [38, 456, 1.0], [38, 457, 1.0], [38, 458, 1.0], [38, 459, 1.0], [38, 460, 1.0], [38, 461, 1.0], [38, 462, 1.0], [38, 463, 1.0], [38, 464, 1.0], [38, 465, 1.0], [38, 466, 1.0], [38, 467, 1.0], [39, 455, 1.0], [39, 456, 1.0], [39, 457, 1.0], [39, 458, 1.0], [39, 459, 1.0], [39, 460, 1.0], [39, 461, 1.0], [39, 462, 1.0], [39, 463, 1.0], [39, 464, 1.0], [39, 465, 1.0], [39, 466, 1.0], [39, 467, 1.0], [40, 455, 1.0], [40, 456, 1.0], [40, 457, 1.0], [40, 458, 1.0], [40, 459, 1.0], [40, 460, 1.0], [40, 461, 1.0], [40, 462, 1.0], [40, 463, 1.0], [40, 464, 1.0], [40, 465, 1.0], [40, 466, 1.0], [41, 455, 1.0], [41, 456, 1.0], [41, 457, 1.0], [41, 458, 1.0], [41, 459, 1.0], [41, 460, 1.0], [41, 461, 1.0], [41, 462, 1.0], [41, 463, 1.0], [41, 464, 1.0], [41, 465, 1.0], [41, 466, 1.0], [42, 455, 1.0], [42, 456, 1.0], [42, 457, 1.0], [42, 458, 1.0], ...] |
| 517473255 | 517473255 | [[41, 493, 1.0], [41, 494, 1.0], [41, 495, 1.0], [41, 496, 1.0], [42, 492, 1.0], [42, 493, 1.0], [42, 494, 1.0], [42, 495, 1.0], [42, 496, 1.0], [42, 497, 1.0], [43, 489, 1.0], [43, 490, 1.0], [43, 491, 1.0], [43, 492, 1.0], [43, 493, 1.0], [43, 494, 1.0], [43, 495, 1.0], [43, 496, 1.0], [43, 497, 1.0], [43, 498, 1.0], [44, 488, 1.0], [44, 489, 1.0], [44, 490, 1.0], [44, 491, 1.0], [44, 492, 1.0], [44, 493, 1.0], [44, 494, 1.0], [44, 495, 1.0], [44, 496, 1.0], [44, 497, 1.0], [44, 498, 1.0], [45, 487, 1.0], [45, 488, 1.0], [45, 489, 1.0], [45, 490, 1.0], [45, 491, 1.0], [45, 492, 1.0], [45, 493, 1.0], [45, 494, 1.0], [45, 495, 1.0], [45, 496, 1.0], [45, 497, 1.0], [45, 498, 1.0], [46, 486, 1.0], [46, 487, 1.0], [46, 488, 1.0], [46, 489, 1.0], [46, 490, 1.0], [46, 491, 1.0], [46, 492, 1.0], [46, 493, 1.0], [46, 494, 1.0], [46, 495, 1.0], [46, 496, 1.0], [46, 497, 1.0], [46, 498, 1.0], [47, 486, 1.0], [47, 487, 1.0], [47, 488, 1.0], [47, 489, 1.0], [47, 490, 1.0], [47, 491, 1.0], [47, 492, 1.0], [47, 493, 1.0], [47, 494, 1.0], [47, 495, 1.0], [47, 496, 1.0], [47, 497, 1.0], [47, 498, 1.0], [47, 499, 1.0], [48, 486, 1.0], [48, 487, 1.0], [48, 488, 1.0], [48, 489, 1.0], [48, 490, 1.0], [48, 491, 1.0], [48, 492, 1.0], [48, 493, 1.0], [48, 494, 1.0], [48, 495, 1.0], [48, 496, 1.0], [48, 497, 1.0], [48, 498, 1.0], [48, 499, 1.0], [49, 486, 1.0], [49, 487, 1.0], [49, 488, 1.0], [49, 489, 1.0], [49, 490, 1.0], [49, 491, 1.0], [49, 492, 1.0], [49, 493, 1.0], [49, 494, 1.0], [49, 495, 1.0], [49, 496, 1.0], [49, 497, 1.0], [49, 498, 1.0], [49, 499, 1.0], [50, 486, 1.0], [50, 487, 1.0], ...] |
... and 170 more row(s).
ImageSegmentation
plane_segmentations
PlaneSegmentation
description: Segmented regions of interest (ROI).
imaging_plane
optical_channel
0
description: An optical channel used to collection light emission during two-photon calcium imaging.
emission_lambda: nan
description: The imaging plane sampled by the two-photon calcium imaging at a depth of {depth} µm.
device
description: A Nikon A1R-MP multiphoton microscope. This system was adapted to provide space to accommodate the behavior apparatus.
manufacturer: Nikon
excitation_lambda: 910.0
indicator: GCaMP6f
location: VISp
conversion: 1.0
unit: meters
origin_coords_unit: meters
grid_spacing
| Data type | float64 |
|---|---|
| Shape | (2,) |
| Array size | 16.00 bytes |
[0.78 0.78]
grid_spacing_unit: micrometers
table
| global_roi_id | pixel_mask | |
|---|---|---|
| id | ||
| 517473350 | 517473350 | [[55, 291, 1.0], [55, 292, 1.0], [56, 290, 1.0], [56, 291, 1.0], [56, 292, 1.0], [56, 293, 1.0], [56, 294, 1.0], [56, 295, 1.0], [56, 296, 1.0], [57, 289, 1.0], [57, 290, 1.0], [57, 291, 1.0], [57, 292, 1.0], [57, 293, 1.0], [57, 294, 1.0], [57, 295, 1.0], [57, 296, 1.0], [57, 297, 1.0], [57, 298, 1.0], [58, 288, 1.0], [58, 289, 1.0], [58, 290, 1.0], [58, 291, 1.0], [58, 292, 1.0], [58, 293, 1.0], [58, 294, 1.0], [58, 295, 1.0], [58, 296, 1.0], [58, 297, 1.0], [58, 298, 1.0], [58, 299, 1.0], [59, 288, 1.0], [59, 289, 1.0], [59, 290, 1.0], [59, 291, 1.0], [59, 292, 1.0], [59, 293, 1.0], [59, 294, 1.0], [59, 295, 1.0], [59, 296, 1.0], [59, 297, 1.0], [59, 298, 1.0], [59, 299, 1.0], [60, 288, 1.0], [60, 289, 1.0], [60, 290, 1.0], [60, 291, 1.0], [60, 292, 1.0], [60, 293, 1.0], [60, 294, 1.0], [60, 295, 1.0], [60, 296, 1.0], [60, 297, 1.0], [60, 298, 1.0], [60, 299, 1.0], [61, 287, 1.0], [61, 288, 1.0], [61, 289, 1.0], [61, 290, 1.0], [61, 291, 1.0], [61, 292, 1.0], [61, 293, 1.0], [61, 294, 1.0], [61, 295, 1.0], [61, 296, 1.0], [61, 297, 1.0], [61, 298, 1.0], [61, 299, 1.0], [62, 287, 1.0], [62, 288, 1.0], [62, 289, 1.0], [62, 290, 1.0], [62, 291, 1.0], [62, 292, 1.0], [62, 293, 1.0], [62, 294, 1.0], [62, 295, 1.0], [62, 296, 1.0], [62, 297, 1.0], [62, 298, 1.0], [62, 299, 1.0], [63, 287, 1.0], [63, 288, 1.0], [63, 289, 1.0], [63, 290, 1.0], [63, 291, 1.0], [63, 292, 1.0], [63, 293, 1.0], [63, 294, 1.0], [63, 295, 1.0], [63, 296, 1.0], [63, 297, 1.0], [63, 298, 1.0], [63, 299, 1.0], [64, 287, 1.0], [64, 288, 1.0], [64, 289, 1.0], [64, 290, 1.0], [64, 291, 1.0], [64, 292, 1.0], ...] |
| 517473341 | 517473341 | [[58, 272, 1.0], [58, 273, 1.0], [58, 274, 1.0], [58, 275, 1.0], [58, 276, 1.0], [58, 277, 1.0], [59, 271, 1.0], [59, 272, 1.0], [59, 273, 1.0], [59, 274, 1.0], [59, 275, 1.0], [59, 276, 1.0], [59, 277, 1.0], [59, 278, 1.0], [59, 279, 1.0], [59, 280, 1.0], [59, 281, 1.0], [59, 282, 1.0], [60, 271, 1.0], [60, 272, 1.0], [60, 273, 1.0], [60, 274, 1.0], [60, 275, 1.0], [60, 276, 1.0], [60, 277, 1.0], [60, 278, 1.0], [60, 279, 1.0], [60, 280, 1.0], [60, 281, 1.0], [60, 282, 1.0], [60, 283, 1.0], [61, 270, 1.0], [61, 271, 1.0], [61, 272, 1.0], [61, 273, 1.0], [61, 274, 1.0], [61, 275, 1.0], [61, 276, 1.0], [61, 277, 1.0], [61, 278, 1.0], [61, 279, 1.0], [61, 280, 1.0], [61, 281, 1.0], [61, 282, 1.0], [62, 270, 1.0], [62, 271, 1.0], [62, 272, 1.0], [62, 273, 1.0], [62, 274, 1.0], [62, 275, 1.0], [62, 276, 1.0], [62, 277, 1.0], [62, 278, 1.0], [62, 279, 1.0], [62, 280, 1.0], [62, 281, 1.0], [62, 282, 1.0], [63, 269, 1.0], [63, 270, 1.0], [63, 271, 1.0], [63, 272, 1.0], [63, 273, 1.0], [63, 274, 1.0], [63, 275, 1.0], [63, 276, 1.0], [63, 277, 1.0], [63, 278, 1.0], [63, 279, 1.0], [63, 280, 1.0], [63, 281, 1.0], [63, 282, 1.0], [64, 268, 1.0], [64, 269, 1.0], [64, 270, 1.0], [64, 271, 1.0], [64, 272, 1.0], [64, 273, 1.0], [64, 274, 1.0], [64, 275, 1.0], [64, 276, 1.0], [64, 277, 1.0], [64, 278, 1.0], [64, 279, 1.0], [64, 280, 1.0], [64, 281, 1.0], [64, 282, 1.0], [65, 268, 1.0], [65, 269, 1.0], [65, 270, 1.0], [65, 271, 1.0], [65, 272, 1.0], [65, 273, 1.0], [65, 274, 1.0], [65, 275, 1.0], [65, 276, 1.0], [65, 277, 1.0], [65, 278, 1.0], [65, 279, 1.0], [65, 280, 1.0], [65, 281, 1.0], ...] |
| 517473313 | 517473313 | [[33, 459, 1.0], [33, 460, 1.0], [33, 461, 1.0], [33, 462, 1.0], [33, 463, 1.0], [34, 458, 1.0], [34, 459, 1.0], [34, 460, 1.0], [34, 461, 1.0], [34, 462, 1.0], [34, 463, 1.0], [34, 464, 1.0], [35, 457, 1.0], [35, 458, 1.0], [35, 459, 1.0], [35, 460, 1.0], [35, 461, 1.0], [35, 462, 1.0], [35, 463, 1.0], [35, 464, 1.0], [35, 465, 1.0], [35, 466, 1.0], [36, 456, 1.0], [36, 457, 1.0], [36, 458, 1.0], [36, 459, 1.0], [36, 460, 1.0], [36, 461, 1.0], [36, 462, 1.0], [36, 463, 1.0], [36, 464, 1.0], [36, 465, 1.0], [36, 466, 1.0], [36, 467, 1.0], [37, 456, 1.0], [37, 457, 1.0], [37, 458, 1.0], [37, 459, 1.0], [37, 460, 1.0], [37, 461, 1.0], [37, 462, 1.0], [37, 463, 1.0], [37, 464, 1.0], [37, 465, 1.0], [37, 466, 1.0], [37, 467, 1.0], [38, 455, 1.0], [38, 456, 1.0], [38, 457, 1.0], [38, 458, 1.0], [38, 459, 1.0], [38, 460, 1.0], [38, 461, 1.0], [38, 462, 1.0], [38, 463, 1.0], [38, 464, 1.0], [38, 465, 1.0], [38, 466, 1.0], [38, 467, 1.0], [39, 455, 1.0], [39, 456, 1.0], [39, 457, 1.0], [39, 458, 1.0], [39, 459, 1.0], [39, 460, 1.0], [39, 461, 1.0], [39, 462, 1.0], [39, 463, 1.0], [39, 464, 1.0], [39, 465, 1.0], [39, 466, 1.0], [39, 467, 1.0], [40, 455, 1.0], [40, 456, 1.0], [40, 457, 1.0], [40, 458, 1.0], [40, 459, 1.0], [40, 460, 1.0], [40, 461, 1.0], [40, 462, 1.0], [40, 463, 1.0], [40, 464, 1.0], [40, 465, 1.0], [40, 466, 1.0], [41, 455, 1.0], [41, 456, 1.0], [41, 457, 1.0], [41, 458, 1.0], [41, 459, 1.0], [41, 460, 1.0], [41, 461, 1.0], [41, 462, 1.0], [41, 463, 1.0], [41, 464, 1.0], [41, 465, 1.0], [41, 466, 1.0], [42, 455, 1.0], [42, 456, 1.0], [42, 457, 1.0], [42, 458, 1.0], ...] |
| 517473255 | 517473255 | [[41, 493, 1.0], [41, 494, 1.0], [41, 495, 1.0], [41, 496, 1.0], [42, 492, 1.0], [42, 493, 1.0], [42, 494, 1.0], [42, 495, 1.0], [42, 496, 1.0], [42, 497, 1.0], [43, 489, 1.0], [43, 490, 1.0], [43, 491, 1.0], [43, 492, 1.0], [43, 493, 1.0], [43, 494, 1.0], [43, 495, 1.0], [43, 496, 1.0], [43, 497, 1.0], [43, 498, 1.0], [44, 488, 1.0], [44, 489, 1.0], [44, 490, 1.0], [44, 491, 1.0], [44, 492, 1.0], [44, 493, 1.0], [44, 494, 1.0], [44, 495, 1.0], [44, 496, 1.0], [44, 497, 1.0], [44, 498, 1.0], [45, 487, 1.0], [45, 488, 1.0], [45, 489, 1.0], [45, 490, 1.0], [45, 491, 1.0], [45, 492, 1.0], [45, 493, 1.0], [45, 494, 1.0], [45, 495, 1.0], [45, 496, 1.0], [45, 497, 1.0], [45, 498, 1.0], [46, 486, 1.0], [46, 487, 1.0], [46, 488, 1.0], [46, 489, 1.0], [46, 490, 1.0], [46, 491, 1.0], [46, 492, 1.0], [46, 493, 1.0], [46, 494, 1.0], [46, 495, 1.0], [46, 496, 1.0], [46, 497, 1.0], [46, 498, 1.0], [47, 486, 1.0], [47, 487, 1.0], [47, 488, 1.0], [47, 489, 1.0], [47, 490, 1.0], [47, 491, 1.0], [47, 492, 1.0], [47, 493, 1.0], [47, 494, 1.0], [47, 495, 1.0], [47, 496, 1.0], [47, 497, 1.0], [47, 498, 1.0], [47, 499, 1.0], [48, 486, 1.0], [48, 487, 1.0], [48, 488, 1.0], [48, 489, 1.0], [48, 490, 1.0], [48, 491, 1.0], [48, 492, 1.0], [48, 493, 1.0], [48, 494, 1.0], [48, 495, 1.0], [48, 496, 1.0], [48, 497, 1.0], [48, 498, 1.0], [48, 499, 1.0], [49, 486, 1.0], [49, 487, 1.0], [49, 488, 1.0], [49, 489, 1.0], [49, 490, 1.0], [49, 491, 1.0], [49, 492, 1.0], [49, 493, 1.0], [49, 494, 1.0], [49, 495, 1.0], [49, 496, 1.0], [49, 497, 1.0], [49, 498, 1.0], [49, 499, 1.0], [50, 486, 1.0], [50, 487, 1.0], ...] |
... and 170 more row(s).
SummaryImages
description: Summary images derived from the two-photon calcium imaging.
images
maximum_intensity_projection
description: Summary image calculated from maximum intensity of the plane.
ContaminationRatios
description: Pre-calculated statistics quantifying the effectiveness of the neuropil subtraction.
table
| ratios | ratios_rmse | |
|---|---|---|
| id | ||
| 0 | 0.078 | 0.003927 |
| 1 | 0.125 | 0.003921 |
| 2 | 0.188 | 0.003701 |
| 3 | 0.165 | 0.003572 |
... and 170 more row(s).
devices
Camera
description: An AVT Mako-G032B camera used to track eye movement and pupil dilation.
manufacturer: Allied Vision
Microscope
description: A Nikon A1R-MP multiphoton microscope. This system was adapted to provide space to accommodate the behavior apparatus.
manufacturer: Nikon
StimulusDisplay
description: An ASUS PA248Q monitor used to display visual stimuli.
manufacturer: ASUS
imaging_planes
ImagingPlane
optical_channel
0
description: An optical channel used to collection light emission during two-photon calcium imaging.
emission_lambda: nan
description: The imaging plane sampled by the two-photon calcium imaging at a depth of {depth} µm.
device
description: A Nikon A1R-MP multiphoton microscope. This system was adapted to provide space to accommodate the behavior apparatus.
manufacturer: Nikon
excitation_lambda: 910.0
indicator: GCaMP6f
location: VISp
conversion: 1.0
unit: meters
origin_coords_unit: meters
grid_spacing
| Data type | float64 |
|---|---|
| Shape | (2,) |
| Array size | 16.00 bytes |
[0.78 0.78]
grid_spacing_unit: micrometers
intervals
epochs
description: Coarse grain experiment structure in the alternating presentations of visual stimuli.
table
| start_time | stop_time | stimulus_type | |
|---|---|---|---|
| id | |||
| 0 | 51.55381 | 531.93378 | static_gratings |
| 1 | 561.98893 | 1042.44259 | natural_scenes |
| 2 | 1047.42969 | 1342.66703 | spontaneous |
| 3 | 1342.70028 | 1823.72944 | natural_scenes |
... and 4 more row(s).
subject
age: P104D
age__reference: birth
description: Mus musculus in vivo.
genotype: Cux2-CreERT2/wt;Camk2a-tTA/wt;Ai93(TITL-GCaMP6f)/Ai93(TITL-GCaMP6f)
sex: M
species: Mus musculus
subject_id: 222426
strain: Cux2-CreERT2;Camk2a-tTA;Ai93-222426
lab_meta_data
ophys_experiment_metadata
ophys_experiment_metadata: {"name":"20160204_222426_3StimB","stimulus_name":"three_session_B","specimen_id":495727015,"specimen":{"rna_integrity_number":null,"weight":9000,"parent_y_coord":null,"parent_x_coord":null,"ephys_result_id":null,"is_cell_specimen":false,"id":495727015,"pinned_radius":null,"sphinx_id":29943,"parent_id":null,"donor":{"mgmt_ihc":null,"donor_race_only_facet":null,"full_genotype":"Cux2-CreERT2\/wt;Camk2a-tTA\/wt;Ai93(TITL-GCaMP6f)\/Ai93(TITL-GCaMP6f)","donor_condition_description_facet":2210967278,"survival_days":null,"tumor_status":null,"molecular_subtype":null,"organism_id":2,"strain":null,"strain_only":"","theiler_stage":null,"id":495727004,"multifocal":null,"weight_grams":30.0,"handedness":null,"age_id":298414311,"pmi":null,"race_only":null,"date_of_birth":"2015-10-24T00:00:00Z","external_donor_name":"222426","chemotherapy":null,"time_to_progression_or_recurrence":null,"extent_of_resection":null,"tags":"Cux2-CreERT2;Camk2a-tTA;Ai93-222426 ","sex_full_name":"Male","transgenic_mouse_id":306,"primary_tissue_source":null,"donor_strain_only_facet":null,"sex":"M","data":null,"name":"Cux2-CreERT2;Camk2a-tTA;Ai93-222426","initial_kps":null,"condition_description":"tissuecyte - Power at Objective (mW) tissuecyte - PMT (V) tissuecyte - Laser Wavelength (nm) tissuecyte - ImageDepth (um)","sleep_state":null,"age":{"name":"P152","tags":"postnatal adulthood adult ","days":152.0,"embryonic":false,"age_group_id":3,"organism_id":2,"id":298414311,"description":null},"transgenic_lines":[{"url_prefix":"http:\/\/www.mmrrc.org\/catalog\/getSDS.jsp?mmrrc_id=","transgenic_line_type_name":"driver","originating_lab":"Mark Mayford and Ulrich Mueller","description":"Scattered expression in restricted populations in cortex, striatum, cortical subplate (amygdala), piriform cortex, and hippocampus.","sub_image_annotation_id":178398161,"id":177837320,"transgenic_line_type_code":"D","transgenic_line_source_name":"MMRRC","stock_number":"031781","url_suffix":null,"ar_association_key_name":"517650087","name":"Camk2a-tTA"},{"url_prefix":"http:\/\/jaxmice.jax.org\/strain\/","transgenic_line_type_name":"reporter","originating_lab":"Allen Institute for Brain Science","description":"Activity of calcium indicator GCaMP6f is dependent on both Cre recombinase activity and activation of the tetO promoter by tTA or rtTA.","sub_image_annotation_id":null,"id":265943423,"transgenic_line_type_code":"R","transgenic_line_source_name":"JAX","stock_number":"024103","url_suffix":".html","ar_association_key_name":"517650087","name":"Ai93(TITL-GCaMP6f)"},{"url_prefix":"http:\/\/www.mmrrc.org\/catalog\/getSDS.jsp?mmrrc_id=","transgenic_line_type_name":"driver","originating_lab":"Ulrich Mueller","description":"Enriched in cortical layers 2\/3\/4, thalamus, midbrain, pons, medulla and cerebellum. ","sub_image_annotation_id":21882,"id":177839004,"transgenic_line_type_code":"D","transgenic_line_source_name":"MMRRC","stock_number":"032779","url_suffix":null,"ar_association_key_name":"517650087","name":"Cux2-CreERT2"}],"smoker":null,"mgmt_methylation":null,"radiation_therapy":null,"pten_deletion":null,"donor_strain_facet":null,"egfr_amplification":null,"donor_sex_facet":4122955671,"recurrence_by_six_months":null},"is_ish":false,"cortex_layer_id":null,"failed_facet":734881840,"treatment_id":null,"tissue_ph":null,"hemisphere":null,"cell_reporter_id":null,"cell_prep_sample_id":null,"data":null,"structure_id":null,"parent_z_coord":null,"name":"Cux2-CreERT2;Camk2a-tTA;Ai93-222426","specimen_id_path":"\/495727015\/","donor_id":495727004,"external_specimen_name":"222426"},"date_of_acquisition":"2016-02-04T17:44:29Z","targeted_structure_id":385,"imaging_depth":175,"storage_directory":"\/external\/neuralcoding\/prod6\/specimen_495727015\/ophys_experiment_501559087\/","experiment_container_id":511510736,"targeted_structure":{"st_level":8,"graph_id":1,"name":"Primary visual area","weight":8690,"acronym":"VISp","parent_structure_id":669,"graph_order":185,"sphinx_id":186,"hemisphere_id":3,"safe_name":"Primary visual area","color_hex_triplet":"08858C","structure_id_path":"\/997\/8\/567\/688\/695\/315\/669\/385\/","failed":false,"depth":7,"neuro_name_structure_id_path":null,"neuro_name_structure_id":null,"structure_name_facet":3425643282,"failed_facet":734881840,"id":385,"ontology_id":1,"atlas_id":755},"fail_eye_tracking":true,"well_known_files":[{"well_known_file_type":{"id":514173041,"name":"OphysExperimentCellRoiMetricsFile"},"attachable_type":"OphysExperiment","download_link":"\/api\/v2\/well_known_file_download\/517090750","well_known_file_type_id":514173041,"path":"\/external\/neuralcoding\/prod6\/specimen_495727015\/ophys_experiment_501559087\/analysis_run_738771288\/501559087_three_session_B_analysis.h5","attachable_id":501559087,"id":517090750},{"well_known_file_type":{"id":739716145,"name":"ObservatoryEventsFile"},"attachable_type":"OphysExperiment","download_link":"\/api\/v2\/well_known_file_download\/739721211","well_known_file_type_id":739716145,"path":"\/external\/neuralcoding\/prod6\/specimen_495727015\/ophys_experiment_501559087\/501559087_events.npz","attachable_id":501559087,"id":739721211},{"well_known_file_type":{"id":514173063,"name":"NWBOphys"},"attachable_type":"OphysExperiment","download_link":"\/api\/v2\/well_known_file_download\/514429113","well_known_file_type_id":514173063,"path":"\/external\/neuralcoding\/prod6\/specimen_495727015\/ophys_experiment_501559087\/501559087.nwb","attachable_id":501559087,"id":514429113}],"id":501559087,"experiment_container":{"weight":6540,"imaging_depth":175,"specimen_id":495727015,"failed_facet":734881840,"failed":false,"targeted_structure_id":385,"id":511510736,"isi_experiment_id":496236971}}
epochs
description: Coarse grain experiment structure in the alternating presentations of visual stimuli.
table
| start_time | stop_time | stimulus_type | |
|---|---|---|---|
| id | |||
| 0 | 51.55381 | 531.93378 | static_gratings |
| 1 | 561.98893 | 1042.44259 | natural_scenes |
| 2 | 1047.42969 | 1342.66703 | spontaneous |
| 3 | 1342.70028 | 1823.72944 | natural_scenes |
... and 4 more row(s).
experiment_description: For more information, please see http://help.brain-map.org/display/observatory/Allen+Brain+Observatory
session_id: 501559087-StimB
institution: Allen Institute for Brain Science
data_collection: Generated by pipeline Brain Observatory version 3.0.
notes: Container ID: 511510736
Mouse ID (from genotype white paper): 222426
Session type: three_session_B
protocol: 20160204_222426_3StimB
Let’s explore:
Maximum projection#
This is the projection of the full motion corrected movie. It shows all of the cells imaged during the session.
max_projection = nwbfile.processing['ophys'].data_interfaces['SummaryImages'].images['maximum_intensity_projection'][:]
fig = plt.figure(figsize=(6,6))
plt.imshow(max_projection, cmap='gray')
plt.axis('off')
(-0.5, 511.5, 511.5, -0.5)
ROI Masks#
ROIs are all of the segmented masks for cell bodies identified in this session. These are stored in the PlaneSegmentation table using a sparse array.
seg = nwbfile.processing["ophys"]["ImageSegmentation"]["PlaneSegmentation"].to_dataframe()
seg.head()
| global_roi_id | pixel_mask | |
|---|---|---|
| id | ||
| 517473350 | 517473350 | [[55, 291, 1.0], [55, 292, 1.0], [56, 290, 1.0... |
| 517473341 | 517473341 | [[58, 272, 1.0], [58, 273, 1.0], [58, 274, 1.0... |
| 517473313 | 517473313 | [[33, 459, 1.0], [33, 460, 1.0], [33, 461, 1.0... |
| 517473255 | 517473255 | [[41, 493, 1.0], [41, 494, 1.0], [41, 495, 1.0... |
| 517471959 | 517471959 | [[19, 346, 1.0], [19, 347, 1.0], [19, 348, 1.0... |
Let’s look at how this is represented. Each mask is a list of (x,y,weight) for only the pixels where the ROI mask is located.
seg['pixel_mask'][517473350]
array([(55, 291, 1.), (55, 292, 1.), (56, 290, 1.), (56, 291, 1.),
(56, 292, 1.), (56, 293, 1.), (56, 294, 1.), (56, 295, 1.),
(56, 296, 1.), (57, 289, 1.), (57, 290, 1.), (57, 291, 1.),
(57, 292, 1.), (57, 293, 1.), (57, 294, 1.), (57, 295, 1.),
(57, 296, 1.), (57, 297, 1.), (57, 298, 1.), (58, 288, 1.),
(58, 289, 1.), (58, 290, 1.), (58, 291, 1.), (58, 292, 1.),
(58, 293, 1.), (58, 294, 1.), (58, 295, 1.), (58, 296, 1.),
(58, 297, 1.), (58, 298, 1.), (58, 299, 1.), (59, 288, 1.),
(59, 289, 1.), (59, 290, 1.), (59, 291, 1.), (59, 292, 1.),
(59, 293, 1.), (59, 294, 1.), (59, 295, 1.), (59, 296, 1.),
(59, 297, 1.), (59, 298, 1.), (59, 299, 1.), (60, 288, 1.),
(60, 289, 1.), (60, 290, 1.), (60, 291, 1.), (60, 292, 1.),
(60, 293, 1.), (60, 294, 1.), (60, 295, 1.), (60, 296, 1.),
(60, 297, 1.), (60, 298, 1.), (60, 299, 1.), (61, 287, 1.),
(61, 288, 1.), (61, 289, 1.), (61, 290, 1.), (61, 291, 1.),
(61, 292, 1.), (61, 293, 1.), (61, 294, 1.), (61, 295, 1.),
(61, 296, 1.), (61, 297, 1.), (61, 298, 1.), (61, 299, 1.),
(62, 287, 1.), (62, 288, 1.), (62, 289, 1.), (62, 290, 1.),
(62, 291, 1.), (62, 292, 1.), (62, 293, 1.), (62, 294, 1.),
(62, 295, 1.), (62, 296, 1.), (62, 297, 1.), (62, 298, 1.),
(62, 299, 1.), (63, 287, 1.), (63, 288, 1.), (63, 289, 1.),
(63, 290, 1.), (63, 291, 1.), (63, 292, 1.), (63, 293, 1.),
(63, 294, 1.), (63, 295, 1.), (63, 296, 1.), (63, 297, 1.),
(63, 298, 1.), (63, 299, 1.), (64, 287, 1.), (64, 288, 1.),
(64, 289, 1.), (64, 290, 1.), (64, 291, 1.), (64, 292, 1.),
(64, 293, 1.), (64, 294, 1.), (64, 295, 1.), (64, 296, 1.),
(64, 297, 1.), (64, 298, 1.), (64, 299, 1.), (64, 300, 1.),
(65, 287, 1.), (65, 288, 1.), (65, 289, 1.), (65, 290, 1.),
(65, 291, 1.), (65, 292, 1.), (65, 293, 1.), (65, 294, 1.),
(65, 295, 1.), (65, 296, 1.), (65, 297, 1.), (65, 298, 1.),
(65, 299, 1.), (65, 300, 1.), (66, 286, 1.), (66, 287, 1.),
(66, 288, 1.), (66, 289, 1.), (66, 290, 1.), (66, 291, 1.),
(66, 292, 1.), (66, 293, 1.), (66, 294, 1.), (66, 295, 1.),
(66, 296, 1.), (66, 297, 1.), (66, 298, 1.), (66, 299, 1.),
(67, 286, 1.), (67, 287, 1.), (67, 288, 1.), (67, 289, 1.),
(67, 290, 1.), (67, 291, 1.), (67, 292, 1.), (67, 293, 1.),
(67, 294, 1.), (67, 295, 1.), (67, 296, 1.), (67, 297, 1.),
(67, 298, 1.), (67, 299, 1.), (68, 287, 1.), (68, 288, 1.),
(68, 289, 1.), (68, 290, 1.), (68, 291, 1.), (68, 292, 1.),
(68, 293, 1.), (68, 294, 1.), (68, 295, 1.), (68, 296, 1.),
(68, 297, 1.), (68, 298, 1.), (69, 287, 1.), (69, 288, 1.),
(69, 289, 1.), (69, 290, 1.), (69, 291, 1.), (69, 292, 1.),
(69, 293, 1.), (69, 294, 1.), (69, 295, 1.), (69, 296, 1.),
(69, 297, 1.), (69, 298, 1.), (70, 287, 1.), (70, 288, 1.),
(70, 289, 1.), (70, 290, 1.), (70, 291, 1.), (70, 292, 1.),
(70, 293, 1.), (70, 294, 1.), (70, 295, 1.), (70, 296, 1.),
(70, 297, 1.), (71, 288, 1.), (71, 289, 1.), (71, 290, 1.),
(71, 291, 1.), (71, 292, 1.), (71, 293, 1.), (71, 294, 1.)],
dtype=[('x', '<u4'), ('y', '<u4'), ('weight', '<f4')])
Plot the masks for all the ROIs.
rois = np.zeros((512,512))
for index,row in seg.iterrows():
for x, y, weight in row.pixel_mask:
rois[int(x), int(y)] = weight
plt.imshow(rois)
<matplotlib.image.AxesImage at 0x7f28611ba230>
Knowing the location of a neuron is valuable if you want to examine the spatial relationships between neurons. For instance, you can calculate the center of an ROI (take the mean of the x and y pixel locations) and use that to measure the distance between two neurons.
Fluorescence and DF/F traces#
The NWB file contains a number of traces reflecting the processing that is done to the extracted fluorescence before we analyze it. The fluorescence traces are the mean fluorescence of all the pixels contained within a ROI mask. In addition to the raw fluorescence, there are also neuropil corrected traces, demixed traces, and DF/F traces.
The signal we are most interested in is the DFF - the change in fluorescence normalized by the baseline fluorescence. The baseline fluorescence was computed as the median fluorescence in a 180s window centered on each time point. The result is the dff trace:
dff_series = nwbfile.processing["ophys"]["DfOverF"]["DfOverF"]
dff = dff_series.data[:].T # Transpose to get (n_cells, n_timepoints)
ts = dff_series.timestamps[:]
fig = plt.figure(figsize=(8,3))
plt.plot(ts, dff[122,:], color='gray')
plt.xlabel("Time (s)")
plt.xlim(1900,2200)
plt.ylabel("DFF")
Text(0, 0.5, 'DFF')
Extracted events#
In addition to these traces, we also provide events extracted from the DF/F traces using the L0 method developed by Sean Jewell and Daniella Witten.
# Get DfOverF events in a RoiResponseSeries
dff_events_series = nwbfile.processing["ophys"]["DfOverF"]["DfOverFEvents"]
dff_events = dff_events_series.data[:].T # Transpose to get (n_cells, n_timepoints)
ts = dff_events_series.timestamps[:]
fig = plt.figure(figsize=(8,3))
plt.plot(ts, dff[122,:], color='gray')
plt.plot(ts, 2*dff_events[122,:]+5, color='black')
plt.xlabel("Time (s)")
plt.xlim(1900,2200)
plt.ylabel("DFF")
Text(0, 0.5, 'DFF')
Stimulus epochs#
Several stimuli are shown during each imaging session, interleaved with each other. The stimulus epoch table provides information of these interleaved stimulus epochs, revealing when each epoch starts and ends. .
stim_epoch = nwbfile.intervals['epochs'].to_dataframe()
stim_epoch
| start_time | stop_time | stimulus_type | |
|---|---|---|---|
| id | |||
| 0 | 51.55381 | 531.93378 | static_gratings |
| 1 | 561.98893 | 1042.44259 | natural_scenes |
| 2 | 1047.42969 | 1342.66703 | spontaneous |
| 3 | 1342.70028 | 1823.72944 | natural_scenes |
| 4 | 1853.75241 | 2334.18960 | static_gratings |
| 5 | 2364.24622 | 2664.51446 | natural_movie_one |
| 6 | 2694.53808 | 3222.69798 | natural_scenes |
| 7 | 3265.25696 | 3805.75971 | static_gratings |
Column |
Description |
|---|---|
start_time |
The time at the start of the epoch |
stop_time |
The time at the end of the epoch |
stimulus_type |
The name of the stimulus for the epoch |
Let’s plot the DFF traces of a number of cells and overlay stimulus epochs.
fig = plt.figure(figsize=(14,8))
#here we plot the first 50 neurons in the session
for i in range(50):
plt.plot(ts, dff[i,:]+(i*2), color='gray')
#here we shade the plot when each stimulus is presented
colors = ['blue','orange','green','red']
for c, stim_name in enumerate(stim_epoch.stimulus_type.unique()):
stim = stim_epoch[stim_epoch.stimulus_type==stim_name]
for j in range(len(stim)):
plt.axvspan(xmin=stim.start_time.iloc[j], xmax=stim.stop_time.iloc[j], color=colors[c], alpha=0.1)
Running speed#
The running speed of the animal on the rotating disk during the entire session.
running_speed_series = nwbfile.processing["behavior"]["BehavioralTimeSeries"]['running_speed']
dxcm = running_speed_series.data[:]
running_ts = running_speed_series.timestamps[:]
Plot the running speed.
plt.plot(running_ts, dxcm)
plt.ylabel("Running speed (cm/s)", fontsize=18)
plt.xlabel("Time (s)", fontsize=18)
Text(0.5, 0, 'Time (s)')
Add the running speed to the neural activity and stimulus epoch figure we made above
fig = plt.figure(figsize=(14,8))
#here we plot the first 50 neurons in the session
for i in range(50):
plt.plot(ts, dff[i,:]+(i*2), color='gray')
#here we shade the plot when each stimulus is presented
colors = ['blue','orange','green','red']
for c, stim_name in enumerate(stim_epoch.stimulus_type.unique()):
stim = stim_epoch[stim_epoch.stimulus_type==stim_name]
for j in range(len(stim)):
plt.axvspan(xmin=stim.start_time.iloc[j], xmax=stim.stop_time.iloc[j], color=colors[c], alpha=0.1)
#here we add the running speed (scaled and offset)
plt.plot(running_ts, (0.2*dxcm)-20)
[<matplotlib.lines.Line2D at 0x7f28609b4850>]
Stimulus Table and Template#
Each stimulus that is shown has a stimulus table that details what each trial is and when it is presented. Additionally, the natural scenes, natural movies, and locally sparse noise stimuli have a stimulus template that shows the exact image that is presented to the mouse. We detail how to access and use these items in Visual stimuli.
Cell ids and indices#
Each neuron in the dataset has a unique id. These IDs are stored in the PlaneSegmentation table we looked at before.
# Cell IDs are stored in the PlaneSegmentation table
plane_seg = nwbfile.processing["ophys"]["ImageSegmentation"]["PlaneSegmentation"]
cell_ids = plane_seg.id[:]
cell_ids
array([517473350, 517473341, 517473313, 517473255, 517471959, 517471769,
517473059, 517471997, 517472716, 517471919, 517472989, 517472293,
517473115, 517472454, 517473020, 517472734, 517474366, 587377483,
517471708, 587377366, 587377223, 517474444, 517474437, 517473105,
517472300, 517472326, 517472708, 517472215, 517472712, 517472360,
517472399, 517472197, 517472582, 517472190, 517473926, 587377518,
517471931, 517472637, 517472416, 517471658, 517472724, 517472684,
517471664, 587377211, 517473947, 587377064, 517472063, 587377621,
517473080, 517472553, 517473001, 517474078, 517471794, 517471674,
517473916, 517471803, 517472592, 517473014, 517474459, 517472241,
517472720, 517472534, 517472054, 587377662, 517474012, 517474020,
517473653, 517472007, 517472645, 517472211, 517472677, 517472731,
517472621, 517472442, 587377204, 517473027, 517472818, 517473304,
517474121, 517473034, 517472909, 517473624, 517472141, 517472129,
517472903, 517472157, 517474423, 517474430, 517472981, 517472352,
517471723, 517472116, 517473957, 517472489, 517472123, 517472438,
517473967, 517474002, 517473991, 517472626, 517473870, 517473374,
587377633, 517473360, 587377495, 587377673, 517473364, 587377651,
587377639, 517472470, 517473110, 517473570, 517472897, 517472207,
517472873, 517471753, 517472563, 517472015, 517472922, 517473980,
517472135, 517472096, 517472913, 517472524, 517471515, 517472916,
517473680, 517472162, 517472388, 517474415, 587377657, 587377167,
517472425, 517472925, 517471912, 587376617, 517472772, 517473098,
517474342, 517473040, 517473369, 517472807, 587376610, 517473089,
517472906, 517472462, 587377108, 517472369, 517472900, 517471744,
517471906, 517472544, 517472503, 517473053, 517472002, 517471785,
517472919, 517472334, 587377507, 517473897, 517471778, 517472020,
517472514, 517473067, 587377006, 517471841, 517472180, 517472477,
587377582, 517473240, 587376723, 517472450, 517473191, 517471925])
Within each individual session, a cell id is associated with an index. This index maps into the dff or event arrays. Pick one cell id from the list above and find the index for that neuron.
target_cell_id = cell_ids[0] # Use first cell as example
cell_index = np.where(cell_ids == target_cell_id)[0]
print(f"Cell ID {target_cell_id} is at index {cell_index}")
Cell ID 517473350 is at index [0]
During data processing, we matched identified ROIs across each of the sessions within experiment containers. Approximately one third of the neurons in the dataset were matched across all three sessions, one third were matched in two of the three session, and one third were only found in one session. When neurons are matched across sessions, that neuron will have the same cell id in all said sessions. This is explored in Cross session data.
How come we don’t always match ROIs across all three session for all neurons?
There are a few factors that could explain why we don’t always match ROIs across all sessions that include biological, experimental, and analytical reasons. Biologically, a neuron must be active within a session to be identifiable during segmentation. For various reasons, a neuron might not be active during some sessions while it is active during others. Experimentally, there are challenges to returning to the precise same field of view. Being at a slightly different depth, or having just a bit of tilt in the imaging plane, might result in some neurons that were in view during one session not being in view during another. Analytically, the method for identifying ROIs as well as for matching ROIs from multiple sessions can make mistakes.