Details for ham34_141-143_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 12:08:52 by Peter Petersen ADMIN
    Updated: 2023-08-14 11:01:06 by Peter Petersen

  • Notes:
    control

Epochs

Epochs Behavioral paradigm Maze type Built maze Manipulation Duration Notes
ham34_141 Homecage_Sleep Homecage Homecage_Mouse
ham34_142 ThetaMaze_AlternativeRunning Theta maze Theta_Maze_Viktor
ham34_143 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_141.csv 1 Head position 100
OptiTrack, Flex 13 ham34_142.csv 2 Head position 100
OptiTrack, Flex 13 ham34_143.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, 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 27 46689

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 27041 4.0023265623029 2 CA1 Pyramidal Cell Deep 4.252801301727 224.60044618351 0.77
2 2870 0.4268631367465 2 CA1 Pyramidal Cell Deep 5.5749128919861 290.60903534486 0.75
3 105878 15.67097622213 2 CA1 Narrow Interneuron Deep 3.862936587393 624.06094198883 0.21
4 4748 0.70386706910034 3 CA1 Pyramidal Cell Deep 2.5273799494524 218.92858384691 0.76
5 5290 0.78380065113535 2 CA1 Wide Interneuron Deep 0.94517958412098 256.47426427 0.79
6 5700 0.84501073934526 4 CA1 Pyramidal Cell Deep 3.1578947368421 127.33911254134 0.76
7 5630 0.83390851543681 3 CA1 Wide Interneuron Deep 0.88809946714032 144.14564703145 0.75
8 2699 0.40150638829912 2 CA1 Wide Interneuron Deep 0 239.62437558647 0.76
9 6489 0.96310012267319 4 CA1 Wide Interneuron Deep 0.61642780089382 171.15432250316 0.77
10 7374 1.0935018445281 3 CA1 Pyramidal Cell Deep 0.5424464334147 154.27819951108 0.67
11 7706 1.1424300923143 3 CA1 Pyramidal Cell Deep 2.2060731897223 125.72996817523 0.68
12 7821 1.1582305027978 4 CA1 Pyramidal Cell Superficial 2.9408004091548 91.603244223133 0.68
13 10276 1.5210814172447 3 CA1 Pyramidal Cell Deep 3.016738030362 115.35470146589 0.77
14 11016 1.6306664168463 3 CA1 Pyramidal Cell Deep 1.2708787218591 83.639843046429 0.63
15 11857 1.7550232637903 2 CA1 Pyramidal Cell Deep 1.1807371173147 123.79917449153 0.76
16 12438 1.8409723993123 3 CA1 Pyramidal Cell Deep 6.9142949027175 155.05102418948 0.72
17 13205 1.957350046568 3 CA1 Wide Interneuron Deep 6.5884134797425 160.71295411735 0.78
18 12953 1.9173711330428 1 CA1 Pyramidal Cell Deep 2.7020767389794 137.61800991914 0.76
19 13855 2.0510871553935 3 CA1 Pyramidal Cell Deep 1.8765788523999 99.981230255584 0.69
20 19023 2.8217772853648 3 CA1 Pyramidal Cell Deep 4.4157073016874 132.20407061379 0.73
21 18929 2.8055392748857 4 CA1 Pyramidal Cell Superficial 5.8111891806223 110.48064121759 0.75
22 44768 6.6268525087676 2 CA1 Narrow Interneuron Deep 0.51375982844889 131.84891787705 0.26
23 46888 6.9399329399822 2 CA1 Narrow Interneuron Deep 0.74645964852414 153.06434259868 0.26
24 100367 14.855653225683 3 CA1 Narrow Interneuron Deep 1.6838203792083 108.03671769162 0.27
25 138235 20.460087399585 1 CA1 Narrow Interneuron Deep 5.577458675444 217.77358601 0.25
26 137405 20.337515730381 4 CA1 Narrow Interneuron Superficial 4.9270405007096 195.06914916257 0.28
27 155948 23.081777559145 2 CA1 Narrow Interneuron Deep 0.96827147510709 279.22009527402 0.26