Details for Peter_MS21_180808_115125_concat
Date & time: 2018-08-08, 11:51:25
Animal subject: MS21
Investigator: Peter Petersen
Experimenters: Michelle Hernandez, Peter Petersen
Project: Theta rhythm perturbation by focal cooling of the septal pacemaker in awake rats
Data repositories: NYUshare_Peter, PeterSetup_DataDrive3, Peter_DataDrive3
Created: 2018-08-20 16:51:30 by Peter Petersen
Updated: 2020-06-26 18:03:53 by Peter Petersen ADMINNotes:
Sleep in homecage in sleepbox. Linear track with slopes (10,-10,0. 3 subsessions).
Epochs
| Epochs | Behavioral paradigm | Maze type | Built maze | Manipulation | Duration | Notes |
|---|---|---|---|---|---|---|
| Peter_MS21_180808_115125 | Homecage_Sleep | Homecage | Homecage_Rat | 5448.528 | pre-sleep in sleepbox | |
| Peter_MS21_180808_132545 | LinearTrack_AlteringSlopes | Linear track | Linear_Track_Peter | Thermal perturbation | 6730.452 | +10 degrees angle. 30 trials without cooling, 30 with. |
| Peter_MS21_180808_145503 | LinearTrack_AlteringSlopes | Linear track | Linear_Track_Peter | Thermal perturbation | 8134.056 | -10 degrees angle. 30 trials without cooling, 40 with. |
| Peter_MS21_180808_164208 | LinearTrack_AlteringSlopes | Linear track | Linear_Track_Peter | Thermal perturbation | 8967.888 | 0 degrees angle. 30 trials without cooling, 30 with. |
| Peter_MS21_180808_165758 | LinearTrack_AlteringSlopes | Linear track | Linear_Track_Peter | Thermal perturbation | 9749.664 | Continuation of previous subsession |
| Peter_MS21_180808_171455 | Homecage_Sleep | Homecage | Homecage_Rat | 13558.212 | post-sleep in sleepbox |
Extracellular
Equipment |
File format |
Sampling rate |
nSamples |
nChannels |
Spike groups |
Least significant bit |
|---|---|---|---|---|---|---|
| Intan Technologies, RHD2000 USB interface board (256ch) | dat | 20000 | 271164000 | 128 | 14 | 0.195 |
Implanted probes
MS21 : #1 Silicon probe NeuroNexus Buzsaki64sp (64 ch, 6 shanks, staggered Non-uniform ) | Region: HIP | Coordinates: -3.3, -2.5, -1.6
MS21 : #2 Silicon probe NeuroNexus Buzsaki64 (64 ch, 8 shanks, staggered) | Region: HIP | Coordinates: -3.3, 2.5, 1.6
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 | 50, 57, 49, 58, 52, 55, 51, 56, 54, 53 | |
| 2 | 60, 37, 59, 35, 62, 34, 61, 33, 64, 63 | |
| 3 | 38, 44, 39, 48, 41, 47, 42, 46, 43, 45 | |
| 4 | 40, 28, 36, 25, 30, 23, 26, 24, 22, 21 | |
| 5 | 27, 6, 29, 5, 32, 4, 31, 3, 1, 2 | |
| 6 | 7, 16, 8, 15, 9, 14, 10, 13, 11, 12 | |
| 7 | 17, 20, 19, 18 | |
| 8 | 114, 121, 113, 122, 116, 119, 115, 120, 118, 117 | |
| 9 | 124, 101, 123, 99, 126, 98, 125, 97, 128, 127 | |
| 10 | 102, 108, 103, 112, 105, 111, 106, 110, 107, 109 | |
| 11 | 104, 92, 100, 89, 94, 87, 90, 88, 86, 85 | |
| 12 | 91, 70, 93, 69, 96, 68, 95, 67, 65, 66 | |
| 13 | 71, 80, 72, 79, 73, 78, 74, 77, 75, 76 | |
| 14 | 81, 84, 83, 82 |
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) | aux | 4 | Temperature | MS temperature probe |
| Intan Technologies, RHD2000 USB interface board (256ch) | adc | 1 | WheelPosition | Running wheel |
| Intan Technologies, RHD2000 USB interface board (256ch) | dig | 1 | OptitrackSync | TTL sync |
| Intan Technologies, RHD2000 USB interface board (256ch) | dig | 2 | BaslerSync | TTL sync |
| Intan Technologies, RHD2000 USB interface board (256ch) | dig | 5, 6, 7, 8 | ArduinoRemote | Remote Button A-D |
| Intan Technologies, RHD2000 USB interface board (256ch) | aux | 1, 2, 3 | Accelerometer | Head mounted accelerometer |
| Intan Technologies, RHD2000 USB interface board (256ch) | adc | 3 | ch_opto_on | |
| Intan Technologies, RHD2000 USB interface board (256ch) | adc | 4 | ch_opto_off |
Equipment |
File names |
Epoch |
Type |
Framerate |
Notes |
|---|---|---|---|---|---|
| OptiTrack, Flex 13 | Take 2018-08-08 01.25.51 PM.csv | 2 | Head position | 120 | |
| OptiTrack, Flex 13 | Take 2018-08-08 02.55.27 PM.csv | 3 | Head position | 120 | |
| OptiTrack, Flex 13 | Take 2018-08-08 04.42.19 PM.csv | 4 | Head position | 120 | |
| OptiTrack, Flex 13 | Take 2018-08-08 04.58.17 PM.csv | 5 | Head position | 120 | |
| Point Grey, Chameleon3 1.3 MP Color USB3 Vision (ON Semi PYTHON 1300) | Basler acA1300-200uc (21965891)_20180808_132550182.avi | 2 | Video | 10 | |
| Point Grey, Chameleon3 1.3 MP Color USB3 Vision (ON Semi PYTHON 1300) | Basler acA1300-200uc (21965891)_20180808_145532552.avi | 3 | Video | 10 | |
| Point Grey, Chameleon3 1.3 MP Color USB3 Vision (ON Semi PYTHON 1300) | Basler acA1300-200uc (21965891)_20180808_164215790.avi | 4 | Video | 10 | |
| Point Grey, Chameleon3 1.3 MP Color USB3 Vision (ON Semi PYTHON 1300) | Basler acA1300-200uc (21965891)_20180808_165815925.avi | 5 | Video | 10 |
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 |
|---|---|---|
| DG – Dentate gyrus (View in Atlas) | 1:64 | |
| CA3 – Field CA3 (View in Atlas) | 65:128 |
Channel tags
Examples and reserved tags: Bad, Good, Theta, Gamma, Delta, Ripple, RippleNoise.
Tag |
Channels |
Spike groups |
|---|---|---|
| Theta | 128 | |
| Cortical | 7,14 | |
| Ripple | 41 | 9 |
| RippleNoise | 74 | |
| Bad | 38,44,39,40,41,36,30,26,37,84,17,81,48 | 6 |
Analysis tags
Tag |
Value |
Description |
|---|---|---|
| OptiTracktracking_offset | 5,-5,0 | |
| linear_track_slope | 10,-10,0 | degrees of incline of linear track |
| CoolingSession | 1 | |
| pos_x_limits | -70,240 | |
| pos_y_limits | -30,30 | |
| sloperecordings | 1,2,2,3,3,5 |
Spike sorting
Method |
Format |
Relative path |
Channels |
Spike sorter |
Notes |
Sorting completed |
Units count |
Sorting ID |
|---|---|---|---|---|---|---|---|---|
| KiloSort | Phy | Kilosort_2018-08-09_143633 | 1:128 | Peter Petersen | Yes | 16 | 10814 |
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 | 31448 | 2.3196191994869 | 8 | CA3 | Pyramidal Cell | Unknown | 4.9287713050114 | 131.46872296395 | 0.63 | 36.100781086532 | |
| 2 | 545660 | 40.24604015338 | 9 | CA3 | Narrow Interneuron | Unknown | 1.0446065315398 | 120.27316839674 | 0.22 | 0 | |
| 3 | 42282 | 3.1188176702508 | 10 | CA3 | Pyramidal Cell | Unknown | 13.197105151128 | 126.38308658093 | 0.66 | 0 | |
| 4 | 385482 | 28.431774991563 | 9 | CA3 | Wide Interneuron | Unknown | 0.018159083952039 | 543.00657095825 | 0.48 | 235.14183408926 | |
| 5 | 21294 | 1.5708555149944 | 8 | CA3 | Pyramidal Cell | Unknown | 1.4558091481168 | 251.2101145083 | 0.65 | 38.728789569615 | |
| 6 | 1753 | 0.12969186156972 | 1 | DG | Pyramidal Cell | Unknown | 2.8522532800913 | 241.94748588244 | 0.6 | 36.315476647708 | |
| 7 | 8390 | 0.61897365241634 | 9 | CA3 | Pyramidal Cell | Unknown | 4.8867699642431 | 124.10962933762 | 0.6 | 51.207618562468 | |
| 8 | 64517 | 4.7590761848048 | 1 | DG | Narrow Interneuron | Unknown | 1.239983260226 | 159.79580669375 | 0.33 | 0 | |
| 9 | 7418 | 0.54743916034375 | 8 | CA3 | Wide Interneuron | Unknown | 0.53922890266918 | 87.374583921144 | 0.7 | 73.243067784334 | |
| 10 | 15324 | 1.1303368904412 | 10 | CA3 | Wide Interneuron | Unknown | 0.13051422605064 | 96.034478144009 | 0.54 | 131.099776756 | |
| 11 | 27887 | 2.058093840747 | 7 | DG | Pyramidal Cell | Unknown | 10.614264711156 | 126.55091670863 | 0.56 | 0 | |
| 12 | 67726 | 4.9969878329109 | 3 | DG | Narrow Interneuron | Unknown | 0.22148067212001 | 122.68354158384 | 0.32 | 241.51420637196 | |
| 13 | 131608 | 9.707001783531 | 8 | CA3 | Narrow Interneuron | Unknown | 0.098778189775698 | 133.96381381183 | 0.34 | 178.0073485167 | |
| 14 | 204181 | 15.066455190299 | 2 | DG | Narrow Interneuron | Unknown | 0.5779186114281 | 175.31267842264 | 0.25 | 0 | |
| 15 | 245549 | 18.110792781664 | 8 | CA3 | Narrow Interneuron | Unknown | 0.089595152087771 | 251.61246357492 | 0.37 | 0 | |
| 16 | 302645 | 22.323084466168 | 3 | DG | Narrow Interneuron | Unknown | 0.69057807001603 | 450.41731052761 | 0.23 | 0 |