Frequently Asked Questions

Here we collect common issues and questions regarding IBLRIG.

First Aid

If your rig is acting up:

• Employ the automated test-script bundled with IBLRIG. This script helps identify common configuration issues. Execute it using PowerShell:

  C:\iblrigv8\venv\scripts\Activate.ps1
  validate_iblrig
  

• Check the comprehensive user manual (“Appendix 3” on GoogleDrive). Verify if all connections are secure, and configurations align with the manual’s guidelines.

• Don’t hesitate to contact our developer team for assistance. We’re committed to getting your system back on track.

Bug Reports & Feature Requests

IBLRIG remains in dynamic development. Your input is invaluable in shaping its direction. Send us your bug reports and feature-requests via GitHub - we will do our best to help you.

Sound Issues

• Double-check all wiring for loose connections.

• Is hardware_settings.yaml set up correctly? Valid options for sound OUTPUT are:

  • hifi,

  • harp,

  • xonar, or

  • sysdefault.

  Make sure that this value matches the actual soundcard used on your rig. Note that sysdefault is only used in test scenarios and should not be used during actual experiments.

Screen Issues

General

• The ribbon cable attaching the screen to the driver board is notoriously finicky. If you are having brightness issues or do not have a signal, try gently repositioning this cable and ensure it is tightly seated in its connection.

• Screen and ribbon cable can be easily damaged. It is useful to have backup at hand.

• Screen flashing can occur if the power supply does not match the screen specifications. Use a 12V adapter with at least 1A.

• If the Bonsai display is appearing on the PC screen when a task starts, try unplugging the rig screen, rebooting and plugging the screen back in. Other variations of screen unplugging and rebooting may also work. Also make sure, that the DISPLAY_IDX value in hardware_settings.yaml is set correctly.

Defining Default Position & Size of Bonsai Visualizers

Is the preview window of the video recording showing on the iPad screen instead of the computer’s main display during a session? To redefine the default position and size of the Bonsai visualizer:

1. Open the Bonsai executable distributed with IBLRIG: C:\iblrigv8\Bonsai\Bonsai.exe.

2. Open the respective Bonsai workflow:

   C:\iblrigv8\devices\camera_recordings\TrainingRig_SaveVideo_TrainingTasks.bonsai
   

3. Start the workflow by clicking on the play-button.

4. Adjust the position and size of the windows as per your preference.

5. Stop the workflow.

6. Save the workflow.

Camera Issues

• If a camera is not detected by the computer or causes intermittent issues it might be an issue with the USB connection.

  • Ensure that the camera is connected to the computer on a USB3 port (usually indicated by a blue plastic tab in the port). USB2 (black tabs) neither provides the necessary transfer rates nor sufficient current to power the camera.

  • Use the original USB3.1 cable provided by FLIR. It comes in 3 m or 5 m - stick with the shorter version if possible.

  • Try to avoid USB extensions. The original cable (see above) should be sufficiently long in most situations.

  • Ideally, use one of the onboard USB3 ports of your computer facing to the back of the machine. Front-facing ports may not be able to provide enough power.

  • If you use a USB 3.1 Host Controller Card check if it requires additional powering through a SATA or Molex cable. FLIR offers a few models that should work fine.

Frame2TTL

• Version 1 of Frame2TTL won’t be detected after restarting the computer. Unplugging and replugging the USB cable should make it responsive again.

• If IBLRIG complains about not receiving any TTL signals from Frame2TTL:

  • Ensure Frame2TTL’s sensor is positioned over the bottom-right corner of the rig’s screen. Secure the sensor’s cable to the screen mount with a zip-tie to prevent it from slipping off the screen. Additionally, use a piece of electrical tape to hold the sensor in place.

  • Verify that the sensor is connected to Frame2TTL with the correct polarity

    • Version 1: GND = black cable, SIG = white cable

    • Version 2 and 3: BLK = black cable, WHT = white cable

  • Ensure that Frame2TTL’s TTL Output is plugged into Bpod’s TTL Input #1. Note that versions 2 and 3 of Frame2TTL have a second BNC output labeled “analog” - this is not the TTL output.

  • Recalibrate Frame2TTL using the calibration routine in IBLRIG’s Tools menu and check for any errors.

• If the above steps do not resolve the issue, try the following:

  1. Swap out the BNC cable between Frame2TTL and Bpod. Use a single cable without any branches.

  2. Connect an oscilloscope to the Bpod end of the cable and run a calibration. Look for a voltage step in Frame2TTL’s output when the calibration routine switches from dark to light.

  3. If you do see the change in the TTL signal, the Bpod might be faulty. Try using a different Bpod unit.

  4. If you do not see the voltage step, the Frame2TTL might be faulty. Try using a different Frame2TTL unit.

Move a mouse onto a previous training stage

Training phases enfold according to an automated procedure, see the mouse training protocol on Figshare for a description of these phases.

However, it is possible that one wants to overwrite the automated progression, and bring back an animal onto a previous training stage.

In this case:

1. Select the training protocol on the GUI

2. Select the wanted training phase manually

   

   Select the training phase manually using the arrows.

On the next day of training, the “automatic” criteria will be computed assuming the training phase last used, i.e. the one you manually selected in this instance.

For example, if you have a mouse on Training Phase 5, and move it manually to Phase 4 (which can be useful when trying to debias an animal), the next session on “automatic” mode will compute the stage progression from stage 4, and disregard the fact that the mouse was on Phase 5 beforehand.