Details for ham34_166-170_amp

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  • Date & time: 2019-02-04, 18:15:23

  • Location: SB1323

  • Animal subject: ham34

  • Investigator: Viktor Varga

  • Experimenters: Viktor Varga

  • Project: Medial Septal place cell generation, Place field-memory field unity of hippocampal neurons

  • Data repositories: NYUshare_Datasets, download session from Web share

  • Created: 2020-01-13 12:16:12 by Peter Petersen ADMIN
    Updated: 2023-08-14 11:04:12 by Peter Petersen

  • Notes:
    real stim: 1.2 s

Epochs

Epochs Behavioral paradigm Maze type Built maze Manipulation Duration Notes
ham34_166 Homecage_Sleep Homecage Homecage_Mouse
ham34_167 ThetaMaze_AlternativeRunning Theta maze Theta_Maze_Viktor Light stimulation
ham34_168 Homecage_Sleep Homecage Homecage_Mouse
ham34_169 Homecage_Sleep Homecage Homecage_Mouse
ham34_170 Homecage_Sleep Homecage Homecage_Mouse

Extracellular

Equipment

File format

Sampling rate

nSamples

nChannels

Spike groups

Least significant bit
Intan Technologies, RHD2000 USB interface board (256ch) dat 20000 64 4 0.195

Implanted probes

HAM34 : Silicon probe NeuroNexus A4x16-Poly2-5mm-23s-200-177 (64 ch, 4 shanks, poly 2 ) | Region: CA1 | 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 26, 23, 21, 28, 22, 27, 19, 30, 20, 29, 17, 32, 18, 31, 24, 25
2 11, 10, 7, 14, 6, 15, 5, 16, 3, 12, 2, 8, 1, 4, 9, 13
3 56, 53, 52, 57, 49, 60, 50, 59, 54, 61, 58, 64, 62, 63, 51, 55
4 41, 40, 38, 43, 37, 44, 36, 45, 35, 46, 34, 47, 33, 48, 39, 42
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 3 opto Analog reading of the opto stimulation
Intan Technologies, RHD2000 USB interface board (256ch) dig 1 optiTrack_sync optiTrack TTL sync

Equipment

File names

Epoch

Type

Framerate

Notes
OptiTrack, Flex 13 ham34_166.csv 1 Head position 100
OptiTrack, Flex 13 ham34_167.csv 2 Head position 100
OptiTrack, Flex 13 ham34_168.csv 3 Head position 100
OptiTrack, Flex 13 ham34_169.csv 4 Head position 100
OptiTrack, Flex 13 ham34_170.csv 5 Head position 100
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
CA1 – Field CA1 (View in Atlas) 1:64

Channel tags

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

Tag

Channels

Spike groups
Theta 32 4
Ripple 32 4

Analysis tags

Tag

Value

Description
prebehaviortime 1
optiTrackExtraPulses 0
useOptitrackTime 0
optiTrack_length_unit 1
opto_pulse_amplitude 0.5
optiTrack_offset -6,58,0
reward_points_linearized 118,192
sessions 1,2,3 Control, Stim, PostStim
timefile 1 time
optiTrack_scaling 0.5

Spike sorting

Method

Format

Relative path

Channels

Spike sorter

Notes

Sorting completed

Units count

Sorting ID
KiloSort Phy Kilosort_Final Viktor Varga Yes 27 46899

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 3454 0.78121424464787 2 CA1 Wide Interneuron Deep 0.57903879559931 373.61860218645 0.71
2 3539 0.42623212684731 2 CA1 Pyramidal Cell Deep 0 279.23898440302 0.77
3 3912 0.4690702516216 4 CA1 Pyramidal Cell Superficial 1.0224948875256 208.9777579322 0.72
4 4681 0.56210765754603 4 CA1 Pyramidal Cell Superficial 2.3499252296518 73.939986994211 0.65
5 6180 0.7489846304415 2 CA1 Wide Interneuron Deep 0 244.45300779301 0.75
6 7650 0.91774330903195 4 CA1 Pyramidal Cell Superficial 1.9607843137255 149.23676389123 0.76
7 10079 1.2085033866602 4 CA1 Pyramidal Cell Superficial 4.5639448357972 132.64671420254 0.77
8 9120 1.0934278136492 4 CA1 Pyramidal Cell Superficial 2.5219298245614 122.98659860447 0.77
9 8481 1.0183996086108 2 CA1 Pyramidal Cell Deep 2.8298549699328 137.29701424752 0.7
10 11937 1.4312834485468 2 CA1 Wide Interneuron Deep 2.0105554159337 121.28782603608 0.73
11 10767 1.2918473442219 2 CA1 Wide Interneuron Deep 2.2290331568682 142.79684819929 0.71
12 11105 1.3316543097121 2 CA1 Pyramidal Cell Deep 2.9716343989194 126.14604904892 0.78
13 12626 1.5136421433842 3 CA1 Pyramidal Cell Deep 5.068905433233 135.57882762965 0.7
14 14548 1.7447516068508 3 CA1 Pyramidal Cell Deep 2.6120428924938 108.93432815967 0.68
15 16737 2.0083540665462 3 CA1 Pyramidal Cell Deep 0.53773077612475 154.74089998674 0.73
16 16911 2.0272730623889 2 CA1 Wide Interneuron Deep 0.17739932588256 193.83601930547 0.7
17 20266 2.4337165744427 4 CA1 Wide Interneuron Superficial 6.0692785946906 146.14171269121 0.81
18 169735 20.343568820615 2 CA1 Narrow Interneuron Deep 0.44186526055322 137.61576474386 0.23
19 144751 17.836991113235 2 CA1 Narrow Interneuron Deep 2.8393586227384 660.50183661667 0.21
20 203407 24.379228988471 4 CA1 Narrow Interneuron Superficial 8.7115979292748 184.56408591196 0.24
21 257449 30.856384247554 2 CA1 Narrow Interneuron Deep 3.0957587716402 286.75718084389 0.23
22 10265 1.2310127599539 3 CA1 Pyramidal Cell Superficial 2.4354603019971 141.98530157927 0.72
23 52528 6.3384422382844 1 CA1 Narrow Interneuron Deep 6.9106000609199 176.2368162237 0.22
24 3775 0.46390339425026 3 CA1 Pyramidal Cell Deep 1.3245033112583 174.06642303945 0.61
25 150519 18.040700507843 3 CA1 Narrow Interneuron Deep 1.0297703279985 136.33963816574 0.24
26 192338 23.054243120393 1 CA1 Narrow Interneuron Deep 9.5976874044651 310.52539579204 0.22
27 47661 19.684481237141 2 CA1 Narrow Interneuron Deep 1.9512809215082 511.17501718722 0.22