[Updated Dec 2015] Integrating a Scanbox-controlled microscope with your system rather pretty straightforward after you understand how the system samples external events and how it can be controlled over the network. Monitoring external TTL events When Scanbox runs it monitors external events on its TTL inputs. Two TTL inputs, labeled TTL0 and TTL1, are readily available as SMA…
Read MoreScanbox cemetery
The final resting place for Scanbox prototypes or cards fried by my esteemed collaborator (don’t let developmental neurobiologists close to electronics.)
Read MorePockels cell modulation via look-up tables
The Scanbox card keeps the laser power per pixel constant across the imaging field despite variations in dwell time during the resonant scanning cycle. It also blanks the laser entirely near the edges of each line. The shape of the modulation signal is fully programmable, although each change requires a firmware update to the board. We achieve…
Read MoreScanbox prototype (circa 2013)
Having done its service with honor for more than a year we had so say our goodbyes to one of only two working models of the original Scanbox prototype. Today we transitioned the two-photon microscope to the latest version of the Scanbox card. Some students and postdocs watched with much concern as cables were being pulled apart. One…
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Download and Install
[Please note that this post is no longer valid] Instructions for downloading and installing Scanbox have now been posted here. The software requires the scanbox card — please do not download if you don’t have one. Use the comments section in this other page to post questions about software/hardware installation.
Read MoreEye Tracking
In addition to tracking the movement of the ball one may want to track eye position along with pupil size. Once again, we use a Dalsa Genie GigE camera to image the eye. Conveniently, it turns out that if you are imaging near 920 nm, there is sufficient light that makes its way through the brain and out of the pupil. Thus, the…
Read MoreBall Tracking
One common way to track the movement of the ball is to use optical mice. Some disadvantages of the method is that mice need to be positioned carefully near the ball surface in each experiment, that at least least two of them are needed to recover all 3 rotation parameters, and that it is not trivial…
Read MoreA Processing Grating Shader
We have been using Processing for displaying visual and auditory stimuli in the Lab for a while. Some of you have ask for examples of full-screen gratings using shaders. So this is not about Scanbox proper, but still useful for those of you studying sensory systems. Below is one demonstration of a drifting sinusoidal grating shader. It…
Read MoreRecursive Image Alignment and Statistics
If it is awake, it will move. And if it moves, your images are likely to do it too. This means that, almost surely, the first step in processing your data will be to align (or register) all the images in the sequence. This is such a basic problem that there are probably as many solutions…
Read MoreSynchronize to the Laser
Scanbox makes sure the data acquisition of the signals from the photo-multipliers are synchronized to the laser pulse. Let me explain why. Suppose you run an asynchronous data acquisition clock at 25Mhz while the laser has a pulse rate of 80Mhz. Then you may obtain images of single cells that look like this: This is…
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