Table of Contents
Research to uncover the neural basis behind Path integration. In this project we use virtual reality with freely moving rodents while recording electrophysiological signal from the Hippocampus CA1. Animals are taught to rear at a visible beacon in the virtual arena, retrieve a randomly distributed reward and go back to the original location where the beacon was, but this time in darkness. We focus on understanding how the animal accumulates vectors as it travels to the reward and then when it needs to retrieve/calculate a correct vector to the original location. In this analysis we focus on proving the rearing behavior at the beacon.
- pip
pip install https://github.com/Fabalinks/Multiple_trial_analysisDuring an experimental session 4 files are generated. Each is a text file and contains columns seperated by space.
position datetime.txt (rotation in quaternion coordinates):
The coordinates are established in the experimental room. When entering the room facing away from the door, X position would be to the right and left of the door (short wall of the arena). The rotation around this axis would be the pitch of the animal. The Z Position is then the second column taken as up and down in height in the room coordinates and the respective rotation around this is the yaw of the animal. With the last position axis the Y rat position would be going futher into the room axis (long arena wall). Hence the rotation around this axis would be the roll of the animal.
| Time | X rat | Z rat (height) | Y rat | rotation_around Y (roll) | rotation_around Z (yaw) | rotation_around X (pitch) | Motive Frame | Motive timestamp | Motive session timestamp |
|---|
beacons_entry.txt (historical): Denotes each time the rat entered the beacon and keeps track of the animal untill it exits and records the amount of time the animal spent in the beacon.
| Time | X rat | Z rat (height) | Y rat | X beacon | Y beacon | time in beacon |
|---|
beacons datetime.txt: Record the trigger of the beacon by the rat.
| Time | X rat | Z rat (height) | Y rat | X beacon | Y beacon |
|---|
metadata date - time.txt : Example described
| Recording started on : | 2021-11-15 16:04:08 |
|---|---|
| Computer time was : | 1636988648.44 s |
| ITI_time : | 1.5 # (s) time after beacon that beacon is inactive (animal cannot just stand there getting beacons, needs to leave |
| time_in_cylinder : | 60 # (s) required time for animal to stay in beacon - if high number, animal needs ot rear for trigger |
| movement_collection_time : | 0.01 # getting position data supposedly at 100hz. |
| animal_ID : | FS11 |
| background_color : | 000 # just black color on the background |
| circle : | 0.075 # (m) radius of visible beacon presented |
| position_change : | 10 # how many beacons till position changes |
| light_off : | 2 # how many beacons till beacon is invisible. If high number = training (always visible)- if 2 evryo toher time invisible |
| Cylinder_color : | grass.png |
| rotation : | 80 #rotation speed for visual perturbation |
| Pellets : | 96 # rewards or trials achieved durign task |
| Beacon : | 217.640997887 # (s) time spent in beacon |
| Sham : | 104.490000248 # (s) time spent in beacon which is in different place and never visible. |
| Distance : | 498.117148451 # in meters |
| Speed : | 31.793808940176444 # cm/s |
| recording lenght : | 1892.398 # (s) |
| high pellets : | 95 # how many pellets were achieved by standing |
| high_time_in_cylinder : | 0.5 # (s) for how long animal has to rear in cylinder to count. |
| invisible_time : | 60 # (s) how long does animal has before beacon becomes visible (time to achieve trial) |
| invisible_count : | 38 # how many invisible beacons animal achieved |
| invisible_list : | [1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 23, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 61, 65, 67, 71, 73, 75, 77, 83, 85, 87, 89, 93, 95] # which beacon number were the invisible ones. |
| Animal jumped : | -1 # how many times did the animal jump? |
| Recording_started_motive : | 0 # Motive - ephys frame number |
| Recording_timestamp_motive : | 0.0 # Motive ephys timestamp |
| Day : | 157 # Which script |
| invisible circle : | 0.15 #(m)how large is the invisible beacon area |
- Fork the Project
- Create your Feature Branch (
git checkout -b analysis/New_stuff) - Commit your Changes (
git commit -m 'Add some New_stuff') - Push to the Branch (
git push origin analysis/New_stuff) - Open a Pull Request
Distributed under the Apache License. See LICENSE.txt for more information.
Fabian Stocek - @fabalinks - [email protected]
Project Link: https://github.com/Fabalinks/Multiple_trial_analysis