PiVR
latest
PiVR: virtual reality for small animals
1. Build your own PiVR
1.1. Standard and High Powered version
1.2. Building the Standard version
1.2.1. Detailed PCB soldering instructions (Standard Version)
1.3. Building the High Powered Version
1.3.1. Detailed PCB soldering instructions (High Power Version)
1.3.2. Testing homogeneity of the stimulation light
1.4. Additional Information
1.4.1. Detailed soldering instructions (cable)
1.4.2. Troubleshooting LEDs
2. Bill of Materials (BOM)
2.1. Standard PiVR setup
2.2. High Powered PiVR setup
3. Step-by-step experimental guide
3.1. Single animal tracking
3.1.1. Select Organism
3.1.2. Define pixel per mm
3.1.3. Setting up the arena and the camera
3.1.4. Animal detection
3.1.5. Animal tracking
3.1.6. After Animal Tracking
3.2. Single animal Tracking with Virtual Reality
3.3. Taking full frame images
3.4. Recording a video
4. Code explanation
4.1. Animal detection
4.1.1. Standard - Mode 1
4.1.2. Pre-Define Background - Mode 2
4.1.3. Reconstruct Background by Stitching - Mode 3
4.2. Animal Tracking
4.3. Head Tail Classification
4.4. Dynamic Virtual Realities
5. PiVR Software Manual
5.1. The Menubar
5.2. The Recording Menu
5.2.1. Camera Control Frame
5.2.2. Experiment Control Frame – Tracking
5.2.3. Experiment Control Frame – VR Arena
5.2.4. Experiment Control Frame – Dynamic VR
5.2.5. Experiment Control Frame – Full Frame Recording
5.2.6. Experiment Control Frame – Timelapse Recording
5.2.7. Experiment Control Frame – Video
5.3. Preparing a Time Dependent Stimulus File
5.4. Set Pixel/mm
5.5. Adjust image
5.5.1. Set up optimal image
5.6. Define Output Files
5.7. Undistort Options
5.8. Define GPIO output channels
5.9. Turn Debug Mode ON/OFF
5.10. Select Animal Detection Mode
5.11. Select Organism
5.12. Updating the software
5.13. High/Low Power LED switch
5.14. Select Body Part for VR stimulation
5.15. Animal Color Selection
6. Explanation of PiVR output
6.1. Tracking
6.1.1. “DATE_TIME_data.csv”
6.1.2. “Background.jpg”
6.1.3. “experiment_settings.json”
6.1.4. “first_frame_data.json”
6.1.5. Optional files
6.1.5.1. “bounding_boxes.npy”
6.1.5.2. “centroids.npy”
6.1.5.3. “midpoints.npy”
6.1.5.4. “heads.npy”
6.1.5.5. “tails.npy”
6.2. VR Arena and Dynamic VR Arena
6.2.1. “DATE_TIME_data.csv”
6.2.2. “RESOLUTION_NAME.csv”
6.2.3. “Background.jpg”
6.2.4. “experiment_settings.json”
6.2.5. “first_frame_data.json”
6.2.6. Optional files
6.2.6.1. “bounding_boxes.npy”
6.2.6.2. “centroids.npy”
6.2.6.3. “midpoints.npy”
6.2.6.4. “heads.npy”
6.2.6.5. “tails.npy”
6.2.6.6. “stimulation.npy”
6.3. Full Frame Recording
6.3.1. “DATE_TIME_data.csv”
6.3.2. Image files
6.3.3. “experiment_settings.json”
6.4. Video
6.4.1. “EXPGRP_VIDEO.h264”
6.4.2. “DATE_TIME_data.csv”
6.4.3. “experiment_settings.json”
6.5. Get started
6.6. Visualization of different points on the animal
7. Tools
7.1. The Menubar
7.2. The Analysis Menu
7.2.1. Distance to source
7.2.2. Distance to source, VR
7.2.3. Single animal tracking (post-hoc)
7.3. The Image Data Handling Menu
7.3.1. Image Seq. to matrix
7.3.2. Video conversion
7.3.3. Undistort Video
7.4. Display tracked experiment
7.4.1. Creation of a video file
7.5. Multi-Animal Tracking
7.5.1. Multi Animal Tracking Output
7.6. Creating a new Virtual Arena
7.7. Creating a new Dynamic Virtual Reality
8. Advanced topics
8.1. Simulate Real-Time Tracking
8.2. Tracking of a new animal
8.3. Create your own undistort files
9. PiVR software installation
9.1. Install PiVR on the Raspberry Pi
9.2. Install PiVR on a PC
9.3. Install PiVR on a Windows 10 PC
9.4. Install PiVR on a Linux PC
9.5. Start PiVR on a PC
10. PiVR software documentation
10.1. PiVR GUI source code
10.2. PiVR Tracking source code
10.2.1. Detection
10.2.2. Tracking
10.2.3. Detection and Tracking Helpers
10.2.4. DefineOutputChannels
10.2.5. Error Messages
10.3. Virtual Arena drawing
10.4. PiVR Analysis source code
10.5. PiVR Image Data Handling source code
11. PiVR Benchmark
11.1. Concepts
11.2. PiVR loop time
11.3. PiVR latency
11.4. PiVR loop time (High Res)
12. FAQ
12.1. Distorted Images
12.2. Progress Bar
12.3. Raspberry Pi does not turn on
12.4. PiVR won’t start a video/experiment
12.5. PiVR software won’t start
12.6. I have camera glitches/interference
13. Contact
13.1. Questions?
13.2. Found a Bug?
13.3. Other questions (scientific, technological, copyright…)
14. Community Building
14.1. Labs using PiVR
14.2. PiVR in the press
14.3. PiVR on blogs
15. Legacy Options
15.1. Preparing a Frame Based Time Dependent Stimulus File
PiVR
Docs
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Overview: module code
All modules for which code is available
VR_drawing_board
analysis_scripts
control_file
fast_tracking
image_data_handling
multi_animal_tracking
output_channels
pre_experiment
start_GUI
tracking_help_classes
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