Details for ham34_123-125_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 12:02:17 by Peter Petersen ADMIN
    Updated: 2023-08-14 10:59:23 by Peter Petersen

  • Notes:
    real stim: 1.2 s

Epochs

Epochs Behavioral paradigm Maze type Built maze Manipulation Duration Notes
ham34_123 Homecage_Sleep Homecage Homecage_Mouse
ham34_124 ThetaMaze_AlternativeRunning Theta maze Theta_Maze_Viktor Light stimulation
ham34_125 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_123.csv 1 Head position 100
OptiTrack, Flex 13 ham34_124.csv 2 Head position 100
OptiTrack, Flex 13 ham34_125.csv 3 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, 60, 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_2019-03-22_122920 Viktor Varga Yes 26 46569

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 1994 0.24853503305703 2 CA1 Pyramidal Cell Deep 0 429.47786533011 0.82
2 2931 0.37286954620803 2 CA1 Wide Interneuron Deep 0 210.8005075316 0.75
3 5644 0.69972485588817 3 CA1 Pyramidal Cell Deep 4.2523033309709 133.48563422546 0.78
4 8746 1.0838331226875 4 CA1 Pyramidal Cell Superficial 5.488223187743 146.98584759758 0.78
5 9630 1.1920761546772 4 CA1 Pyramidal Cell Superficial 0.93457943925234 262.78627507563 0.77
6 24195 2.9939466222936 3 CA1 Pyramidal Cell Deep 5.6209960735689 97.907793459649 0.69
7 47794 5.9140841003696 3 CA1 Pyramidal Cell Deep 7.992635058794 120.51287595576 0.64
8 152856 18.913201039046 3 CA1 Narrow Interneuron Deep 2.6822630449573 150.76732619873 0.28
9 1719 0.21964822920818 3 CA1 Pyramidal Cell Deep 0.58173356602676 214.43277308128 0.79
10 159086 19.685072131567 2 CA1 Narrow Interneuron Deep 2.1434947135512 522.68725835735 0.21
11 9166 1.1427806843783 4 CA1 Pyramidal Cell Superficial 3.2729653065678 405.30354326927 0.75
12 10514 1.3055394732728 3 CA1 Pyramidal Cell Deep 2.1875594445501 125.43916916623 0.64
13 8692 1.0773123770544 4 CA1 Pyramidal Cell Superficial 4.6019328117809 109.04352128663 0.77
14 12412 1.5362489842247 4 CA1 Pyramidal Cell Superficial 2.8198517563648 104.36360669096 0.74
15 17890 2.217028391558 3 CA1 Pyramidal Cell Deep 0.78256008943544 133.22054863408 0.77
16 24429 3.0228397014488 2 CA1 Narrow Interneuron Deep 0.85963404150804 156.083357929 0.28
17 31045 3.8414428115209 2 CA1 Pyramidal Cell Deep 4.7672733129328 137.14849407796 0.75
18 35120 4.3462580905201 2 CA1 Pyramidal Cell Deep 3.5876993166287 269.97791720724 0.76
19 171138 21.175004511836 4 CA1 Narrow Interneuron Superficial 2.3957274246515 271.27796966213 0.24
20 3766 0.46745437652733 4 CA1 Wide Interneuron Superficial 1.327668613914 136.21765241367 0.74
21 3333 0.412864391148 4 CA1 Pyramidal Cell Superficial 3.000300030003 171.72961939757 0.71
22 7520 0.93056045868315 4 CA1 Pyramidal Cell Superficial 0.39893617021277 73.146093309024 0.61
23 5578 0.6906726595129 2 CA1 Pyramidal Cell Deep 1.0756543564001 197.91158576415 0.71
24 9602 1.1882632753832 2 CA1 Pyramidal Cell Deep 1.4580295771714 124.99858901268 0.78
25 30455 3.7684329563327 3 CA1 Pyramidal Cell Deep 5.7461828927926 115.27857289632 0.65
26 254714 31.515743064154 2 CA1 Narrow Interneuron Deep 0.98149296858437 315.43375570661 0.27