Details for ham34_156-158_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 12:20:48 by Peter Petersen ADMIN
    Updated: 2023-08-14 11:03:29 by Peter Petersen

  • Notes:
    control

Epochs

Epochs Behavioral paradigm Maze type Built maze Manipulation Duration Notes
ham34_156 Homecage_Sleep Homecage Homecage_Mouse
ham34_157 ThetaMaze_AlternativeRunning Theta maze Theta_Maze_Viktor
ham34_158 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_156.csv 1 Head position 100
OptiTrack, Flex 13 ham34_157.csv 2 Head position 100
OptiTrack, Flex 13 ham34_158.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, 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 46965

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 2776 0.41449963007476 4 CA1 Pyramidal Cell Superficial 1.8011527377522 134.18042851288 0.78
2 3042 0.45431197169992 4 CA1 Wide Interneuron Superficial 4.6022353714661 273.97360673309 0.76
3 3810 0.56690275314462 4 CA1 Pyramidal Cell Superficial 2.0997375328084 187.87136729791 0.71
4 4771 0.71042475135915 2 CA1 Pyramidal Cell Deep 0 270.54785847884 0.77
5 6206 0.92405154673997 4 CA1 Pyramidal Cell Superficial 3.8672252658717 116.90119375645 0.69
6 6017 0.90011100745781 2 CA1 Pyramidal Cell Deep 2.4929366794083 221.97831486267 0.72
7 6327 0.94125502008256 2 CA1 Wide Interneuron Deep 1.7385806859491 203.76195353751 0.75
8 6493 0.96630373277715 4 CA1 Wide Interneuron Superficial 2.9262282458032 140.4854343502 0.78
9 6880 1.0253542917638 2 CA1 Wide Interneuron Deep 0.72674418604651 150.05314470165 0.76
10 7138 1.0624486888114 4 CA1 Wide Interneuron Superficial 2.5217147660409 112.75089803244 0.78
11 7078 1.0526721494308 1 CA1 Pyramidal Cell Superficial 5.08618253744 102.80019340966 0.79
12 8735 1.2990899952662 3 CA1 Wide Interneuron Deep 2.5186033199771 137.43424307782 0.67
13 9686 1.4416989006041 2 CA1 Pyramidal Cell Deep 0.20648358455503 144.08845832022 0.71
14 10761 1.6355204958486 4 CA1 Pyramidal Cell Superficial 9.9433138184184 206.0714372473 0.78
15 12310 1.8300094417932 3 CA1 Pyramidal Cell Deep 8.2047116165719 85.178657965979 0.64
16 14054 2.0892032557885 2 CA1 Pyramidal Cell Deep 2.9884730325886 128.78681117128 0.76
17 15831 2.3536997946233 3 CA1 Pyramidal Cell Superficial 2.0845177184006 132.05269705953 0.71
18 19843 2.9492833693251 3 CA1 Pyramidal Cell Superficial 8.2144836970216 97.741401276252 0.77
19 19852 2.9515801030286 3 CA1 Pyramidal Cell Superficial 1.0578279266573 163.5525227835 0.78
20 36113 5.3703587944101 3 CA1 Pyramidal Cell Superficial 4.3474649018359 133.09283351101 0.65
21 26468 3.9337430625663 1 CA1 Wide Interneuron Superficial 0.64228502342451 118.09724099143 0.76
22 147994 21.994568221171 2 CA1 Narrow Interneuron Deep 8.9125234806816 723.04888965179 0.19
23 72005 10.701371658586 2 CA1 Narrow Interneuron Deep 0.43052565794042 158.34224881937 0.23
24 183450 27.264358677151 1 CA1 Narrow Interneuron Superficial 9.577541564459 206.45976318885 0.24
25 247901 36.842670756489 2 CA1 Narrow Interneuron Deep 3.9209200446953 329.96161906045 0.22
26 154376 22.943112395577 3 CA1 Narrow Interneuron Superficial 3.5562522671918 160.38195828717 0.25
27 204019 30.320971693075 4 CA1 Narrow Interneuron Superficial 10.837225944642 233.3329877838 0.23