Details for ham34_162-165_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 12:22:52 by Peter Petersen ADMIN
    Updated: 2023-08-14 11:03:49 by Peter Petersen

  • Notes:
    control

Epochs

Epochs Behavioral paradigm Maze type Built maze Manipulation Duration Notes
ham34_162 Homecage_Sleep Homecage Homecage_Mouse
ham34_163 ThetaMaze_AlternativeRunning Theta maze Theta_Maze_Viktor
ham34_164 Homecage_Sleep Homecage Homecage_Mouse
ham34_165 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_162.csv 1 Head position 100
OptiTrack, Flex 13 ham34_163.csv 2 Head position 100
OptiTrack, Flex 13 ham34_164.csv 3 Head position 100
OptiTrack, Flex 13 ham34_165.csv 4 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 -5, 62, 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 25 47025

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 2692 0.42452573816207 2 CA1 Pyramidal Cell Superficial 0 221.67778395732 0.77
2 7254 1.1573107687408 2 CA1 Pyramidal Cell Superficial 0.82712985938792 242.04879321572 0.73
3 5428 0.85490225768457 1 CA1 Wide Interneuron Deep 2.210759027266 95.919087202029 0.79
4 13399 2.115798359537 2 CA1 Wide Interneuron Superficial 2.1643406224345 181.43357942624 0.66
5 10627 1.6701438410794 4 CA1 Wide Interneuron Superficial 3.6698974310718 136.3247235147 0.78
6 15177 2.3907844545483 4 CA1 Pyramidal Cell Superficial 4.0192396389273 141.10568039022 0.73
7 10758 1.692575490393 2 CA1 Pyramidal Cell Superficial 1.8590816136828 134.74853722631 0.71
8 19218 3.0198683626213 4 CA1 Pyramidal Cell Superficial 3.8505567696951 86.326780130956 0.65
9 198252 31.14715234514 2 CA1 Narrow Interneuron Superficial 5.0440853055707 698.51457404482 0.21
10 160241 25.175339196655 3 CA1 Narrow Interneuron Superficial 4.387141867562 139.64527913703 0.27
11 1416 0.2235447179659 2 CA1 Pyramidal Cell Superficial 0 414.65838530694 0.74
12 1394 0.22068481109004 2 CA1 Pyramidal Cell Superficial 1.4347202295552 216.32984881079 0.71
13 4734 0.74397381212181 2 CA1 Wide Interneuron Superficial 0.63371356147022 140.67350297858 0.7
14 3861 0.60706589322918 3 CA1 Pyramidal Cell Superficial 1.5540015540016 95.126694690482 0.66
15 10198 1.603291618378 2 CA1 Narrow Interneuron Superficial 0.098058442831928 184.10271911707 0.23
16 12724 1.9997043191052 4 CA1 Pyramidal Cell Superficial 1.4932411191449 168.88926333731 0.77
17 13065 2.0538134332226 2 CA1 Pyramidal Cell Superficial 3.5973976272484 128.2778285647 0.75
18 14910 2.3471795438155 1 CA1 Wide Interneuron Deep 1.3413816230718 133.05522553622 0.75
19 14254 2.2405637707377 3 CA1 Wide Interneuron Superficial 3.5077872877789 91.031078406461 0.74
20 27340 4.2955435456131 3 CA1 Pyramidal Cell Superficial 5.7790782735918 81.21629309536 0.57
21 15338 2.4109089906534 3 CA1 Pyramidal Cell Superficial 2.8034945886035 120.06576231306 0.73
22 15517 2.4379916112003 3 CA1 Wide Interneuron Superficial 2.0622543017336 102.96491919773 0.75
23 21084 3.3177762609332 3 CA1 Pyramidal Cell Superficial 2.0394612028078 136.45448878946 0.67
24 31789 4.9959260862252 3 CA1 Wide Interneuron Superficial 1.5099562741829 125.08749491404 0.7
25 251342 39.488081179836 2 CA1 Narrow Interneuron Superficial 2.6020322906637 304.06833465834 0.22