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/Rearing_analysisDuring an experimental session 3 files are generated.
position datetime.txt (rotation in quaternion coordinates):
| Time | X rat | Z rat | Y rat | X rotation_rat | Y rotation_rat | Z rotation_rat | Motive Frame | Motive timestamp | Motive session timestamp |
|---|
beacons datetime.txt:
| Time | X rat | Z rat | Y rat | X beacon | Y beacon |
|---|
metadata datetime.txt
self explanatory text file that can be machine read out
20210505_Calibration_arena_movement Calculating vestibular/ physical displacement of the arena.
20210507_Positions_together Moving of event files together
20210512_File_moving Moving of ephys files together.
20210517_FS_Joining_txt_frame_number Create spreadsheet with events and frame numbers for ephys sync
20210525_FS_Borderless_rears Looking at trajectories, rear and events only inside the boundary of arena - redundant later
20210525_FS_Identify_invisible_beacon getting only invisible beacon time out
20210525_FS_LT_Performance_FS03-FS06 Plotting Long Term performance of each rat with beacon metrics
20210525_FS_Z_Time_FS03_FS06 Identify time spent rearing and graph
20210526_FS_rearing_histogram Creates a data frame including all events with all information about trial to be exported and analysed later
20210628_FS_Calibration_File_visualization Uses predetected file for calibration settings which are then hardcoded
20210706_FS_rearing_fatigue Calculating fatigue in a trial - not finished
20210811_FS_Normalize_occupancy_bins Use area estimation to be able to normalize rearing attempts within a given beacon position - uses file from 20210526_FS_rearing_histogram
20210811_FS_Plotting_Normalize_occupancy_bins Plots histogram of rears around beacon which is normalized.
20211108_FS_visualize_radius Plots area differences between circle sizes.
20211111_FS_Normalization_problem Simplified to solve normalization problem.
20211125_FS_rearing_dynamics_simple Makes a Dataframe with rear events and trajectories surrounding it.
20211201_FS_rearing_dynamics_PLOTTING Plotting of the rearing dynamics around beacon for progress report
20211708_FS_Pseudorandom_disttribution making the next beacon to be pseudorandomly assigned at least x cm away from last one.
- 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 - stocek@bio.lmu.de
Project Link: https://github.com/Fabalinks/Rearing_analysis