Details for ham34_100-102_amp
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 11:56:56 by Peter Petersen ADMIN
Updated: 2023-08-14 10:58:56 by Peter PetersenNotes:
Stimulation on central arm and one of the side arms
Epochs
| Epochs | Behavioral paradigm | Maze type | Built maze | Manipulation | Duration | Notes |
|---|---|---|---|---|---|---|
| ham34_100 | Homecage_Sleep | Homecage | Homecage_Mouse | |||
| ham34_101 | ThetaMaze_AlternativeRunning | Theta maze | Theta_Maze_Viktor | Light stimulation | ||
| ham34_102 | 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_100.csv | 1 | Head position | 100 | |
| OptiTrack, Flex 13 | ham34_101.csv | 2 | Head position | 100 | |
| OptiTrack, Flex 13 | ham34_102.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_2019-03-20_183834 | Viktor Varga | Yes | 18 | 46447 |
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 | 6094 | 0.96345009613869 | 3 | CA1 | Pyramidal Cell | Deep | 2.9537249753856 | 143.58109830337 | 0.78 | ||
| 2 | 24530 | 3.8776886882446 | 4 | CA1 | Pyramidal Cell | Superficial | 1.1414594374236 | 91.508197085244 | 0.73 | ||
| 3 | 27953 | 4.4131567929579 | 3 | CA1 | Pyramidal Cell | Deep | 3.3627875362215 | 134.13620456218 | 0.69 | ||
| 4 | 130978 | 20.678926782993 | 4 | CA1 | Narrow Interneuron | Superficial | 2.9088854616806 | 336.36054328555 | 0.28 | ||
| 5 | 108647 | 17.153263510334 | 3 | CA1 | Narrow Interneuron | Deep | 1.435842683185 | 222.82929461583 | 0.25 | ||
| 6 | 3982 | 0.6338507903142 | 4 | CA1 | Wide Interneuron | Superficial | 0.75339025615269 | 298.91087930468 | 0.7 | ||
| 7 | 4323 | 0.6826276474619 | 3 | CA1 | Pyramidal Cell | Deep | 0 | 82.946372017941 | 0.67 | ||
| 8 | 4341 | 0.68660012392175 | 4 | CA1 | Pyramidal Cell | Superficial | 0 | 265.43859338032 | 0.79 | ||
| 9 | 5393 | 0.85508100453642 | 4 | CA1 | Wide Interneuron | Superficial | 1.6688299647691 | 233.6999593159 | 0.76 | ||
| 10 | 6471 | 1.0254177057882 | 4 | CA1 | Pyramidal Cell | Superficial | 0.30907124092103 | 141.70195346375 | 0.75 | ||
| 11 | 7161 | 1.1347520337827 | 3 | CA1 | Wide Interneuron | Deep | 0.13964530093562 | 285.12901530169 | 0.79 | ||
| 12 | 8438 | 1.3338563479236 | 3 | CA1 | Wide Interneuron | Deep | 0.23702299123015 | 231.85764494435 | 0.79 | ||
| 13 | 9478 | 1.4974375065122 | 4 | CA1 | Pyramidal Cell | Superficial | 3.2707322219878 | 152.40496146135 | 0.75 | ||
| 14 | 10621 | 1.6831319153252 | 3 | CA1 | Pyramidal Cell | Deep | 0.56491855757462 | 109.19959492261 | 0.75 | ||
| 15 | 11731 | 1.8556850019713 | 3 | CA1 | Pyramidal Cell | Deep | 3.6655016622624 | 138.97435477287 | 0.74 | ||
| 16 | 14625 | 2.3112846731815 | 3 | CA1 | Pyramidal Cell | Deep | 1.2991452991453 | 182.09335036297 | 0.77 | ||
| 17 | 14886 | 2.3560039574093 | 3 | CA1 | Wide Interneuron | Deep | 0.13435442697837 | 233.57459915307 | 0.71 | ||
| 18 | 175522 | 27.710926420719 | 2 | CA1 | Narrow Interneuron | Deep | 2.8999213773772 | 302.20907988703 | 0.29 |