Details for 20160505

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  • Date & time: 2016-02-10,

  • Animal subject: PV3

  • Investigator: Sam McKenzie

  • Experimenters: Dan English, Sam McKenzie

  • Project: Ground truth cell-types using various opto-tag approaches

  • Data repositories: NYUshare_Datasets, download session from Web share

  • Created: 2019-04-02 15:29:27 by Peter Petersen ADMIN
    Updated: 2020-06-27 18:44:00 by Peter Petersen ADMIN

  • Notes:
    Optotagging in homecage

Epochs

Epochs Behavioral paradigm Maze type Built maze Manipulation Duration Notes
20160210 Homecage_Sleep Homecage Homecage_Mouse Light stimulation 29708.208

Extracellular

Equipment

File format

Sampling rate

nSamples

nChannels

Spike groups

Least significant bit
Intan Technologies, RHD2000 USB interface board (256ch) dat 20000 594164160 32 4 0.195

Implanted probes

PV3 : Silicon probe Euisik Yoon, University of Michigan μLED 12LED (32 ch, 4 shanks, staggered Custom) | Region: HIP | Coordinates: , ,

Spike groups

Spike groups are typically defined by the group of channels within shanks. Channels are listed and comma-separated and labels can further be assigned to each group. Channels are 0-indexed.

Group

Channels

Label
1 21, 25, 22, 26, 28, 24, 27, 23
2 17, 29, 18, 30, 32, 20, 31, 19
3 13, 1, 14, 2, 16, 3
4 9, 5, 10, 6, 8, 12, 7, 11
This section is dedicated to extra inputs besides the primary recording channels. For extracellular recordings this includes any extra analog and digital channels. Further it can be inputs saved with an Arduino or Raspberry pi or an entirely different hardware solution.

Equipment

Input type

Channel

Tag

Description
Intan Technologies, RHD2000 USB interface board (256ch) adc 0 StimShank1
Intan Technologies, RHD2000 USB interface board (256ch) adc 1 StimShank1
Intan Technologies, RHD2000 USB interface board (256ch) adc 2 StimShank3
Intan Technologies, RHD2000 USB interface board (256ch) adc 3 StimShank4

Equipment

File names

Epoch

Type

Framerate

Notes
Brain regions are defined according to the Allen Institute Atlas. A brain region can be assigned to a list of channels or spike groups.

Brain region

Channels

Spike groups
HIP – Hippocampal region (View in Atlas) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64

Channel tags

Examples and reserved tags: Bad, Good, Theta, Gamma, Delta, Ripple, RippleNoise.

Tag

Channels

Spike groups
Bad 4, 15 1, 2
Theta 8 4
Ripple 8 4

Analysis tags

Tag

Value

Description

Spike sorting

Method

Format

Relative path

Channels

Spike sorter

Notes

Sorting completed

Units count

Sorting ID
Klustakwik Neurosuite Sam McKenzie Yes 30 28078

Spike sorted units

# Spike count Firing rate (Hz) Spike group Brain region Cell type Deep/Superficial Refractory violation (‰) Peak voltage (µV) Trough-to-Peak (ms) Isolation distance
1 96855 3.2604487624719 4 HIP Pyramidal Cell Superficial 2.5708533374632 379.45963032924 0.58 61.380625332207
2 31669 1.0674424599421 4 HIP Pyramidal Cell Superficial 1.5156777921627 272.89758173455 0.7 23.851379522738
3 50552 1.7023508189528 4 HIP Pyramidal Cell Deep 11.137047001108 161.45150612072 0.63 22.373184323282
4 44172 1.4871754024084 4 HIP Wide Interneuron Deep 2.6487367563162 131.40172133173 0.33 53.190477983095
5 182710 6.1502754244374 4 HIP Pyramidal Cell Deep 14.257566635652 231.04623305303 0.66 63.434574456303
6 33263 1.1218160497689 4 HIP Pyramidal Cell Superficial 2.4351381414785 335.33675412597 0.63 38.898618031875
7 7880 0.26554359473929 4 HIP Pyramidal Cell Deep 2.1573604060914 266.05387777808 0.68 16.157046206034
8 49363 1.6624971234544 4 HIP Pyramidal Cell Superficial 8.3260741851184 187.9366718807 0.58 20.315482882328
9 104205 3.5077779063135 4 HIP Pyramidal Cell Superficial 3.5123074708507 174.64125313036 0.5 26.703556192736
10 41135 1.3846483623716 4 HIP Pyramidal Cell Superficial 4.0111826911389 228.85805596535 0.55 23.875757057123
11 139934 4.7103101923926 4 HIP Pyramidal Cell Deep 1.8365801020481 154.42092275528 0.47 64.565582883038
12 93991 3.163972874885 4 HIP Pyramidal Cell Superficial 7.7135044844719 213.11794031939 0.58 25.951533090833
13 37251 1.2540889820218 4 HIP Pyramidal Cell Superficial 4.6710155432069 203.05860312483 0.56 16.712543738102
14 72490 2.4402020805098 4 HIP Pyramidal Cell Superficial 11.560215202097 158.91247203108 0.59 49.053824093034
15 26238 0.88436790840195 4 HIP Pyramidal Cell Deep 2.6678862718195 182.61496307714 0.6 19.253493503329
16 119889 4.0356316562327 4 HIP Pyramidal Cell Superficial 8.7080549508295 266.11185229234 0.55 31.383445534545
17 6000 0.20208290998016 3 HIP Pyramidal Cell Deep 1 103.92376580479 0.7 24.300519129587
18 2652 0.090079765122515 3 HIP Pyramidal Cell Deep 0.37707390648567 178.43867600674 0.66 24.342987500038
19 23292 0.78436923456347 3 HIP Pyramidal Cell Deep 2.404258973038 204.90882769546 0.61 33.156658857647
20 19086 0.64265861194023 3 HIP Pyramidal Cell Deep 1.8861993083936 295.79952580647 0.69 24.318698727694
21 20059 0.67544812193828 3 HIP Pyramidal Cell Deep 1.894411486116 268.62233299848 0.65 35.88642758073
22 465341 15.666235999845 3 HIP Narrow Interneuron Deep 3.1654206270241 197.46275443461 0.29 234.69647506527
23 685911 23.092098947401 3 HIP Narrow Interneuron Deep 7.9543847525408 260.49886517721 0.23 300.98800253355
24 7232 0.24398980482258 3 HIP Pyramidal Cell Deep 0.13827433628319 190.98684609162 0.59 64.804133561289
25 8424 0.28371297139258 3 HIP Wide Interneuron Deep 0.35612535612536 170.26821865116 0.12 41.41846805946
26 63099 2.1242357810215 3 HIP Pyramidal Cell Deep 3.5658251319355 169.57747451376 0.59 95.616620519391
27 47436 1.5968778190677 3 HIP Pyramidal Cell Deep 3.1199932540686 156.59591093225 0.64 209.450440824
28 1958 0.06630587466189 3 HIP Pyramidal Cell Deep 0 184.57349428595 0.56 29.314341578729
29 22642 0.76254263412173 3 HIP Pyramidal Cell Deep 1.94329122869 207.92956989329 0.7 22.145858163338
30 55938 1.8830310165771 3 HIP Pyramidal Cell Deep 5.291572812757 166.17461622172 0.59 57.364550113847