We previously describe how we can incorporate DeepLabCut models to run concurrently to Scanbox to provide real-time pose estimation while imaging. Of course, the mechanism for communicating with DeepLabCut is general enough to allow processing by other means. In some simple cases, just as detecting the center of the pupil doing two-photon imaging, simple image…
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Real-time imaging and pose estimation
I’ve made substantial progress to read real-time DeepLabCut Live date (see paper by Kane et al here) from Scanbox. As you can see in the example below, I got to the point where we can do two-photon imaging and pose estimation in real time. As you recall, the behavior cameras in Scanbox are triggered once…
Read MoreEvent Panel
An updated event panel provides real-time information about TTL events and allows you to provide a name, which is then used to create a matching field in the file metadata. First, this allows for the user to detect if all required events are coming in as expected during the experiment (as opposed to finding out…
Read MoreUsing USB3 cameras with Scanbox
Scanbox has long supported the use of GigE cameras for behavior, but integrating USB3 cameras which support an external trigger is also possible. As an example, consider the Mako-U series. Wire up the camera To use one of these cameras you have to be using a trigger cable. Different manufacturers offer cables that differ in…
Read MoreSimultaneous imaging with port and behavior cameras
If you have one of the new systems (aka as the pizza box) you can now acquire imagery simultaneously from the port camera and the behavior cameras. During 2p imaging the behavior cameras are triggered at the beginning of a frame (TTL OUT 1x f.r.) or at the beginning and middle of a frame (TTL…
Read MoreA simple lick-o-meter and liquid reward delivery system
Some behavioral experiments reward correct performance. A typical response is a lick of a spout and the reward is a fixed volume of water. One simple way to achieve this is by using an Arduino board along with the capacitive sensing library. The diagram below summarizes the parts used. Just connect a 1 Mohm resistor between pins…
Read MoreUsing the quadrature encoder to track locomotion
Scanbox allows you to acquire the position of a rotating platform at each frame of the microscope. To do so, you need a quadrature encoder to be mounted on the axis of your platform. We use the US Digital HS-360-IE-S, but any quadrature encoder will do as well. The encoder needs to be wired to an Arduino…
Read MoreBlanking the laser between trials
Sometimes, during long behavioral sessions, it is advantageous to turn off the laser between trials to minimize damage while keeping the microscope scanning. To do this without introducing any additional noise that may influence the behavioral state we use the Pockels cell. Scanbox now allows one to blank the laser by sending a command over…
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