Scanbox includes some basic processing functions that you can use to (a) align the images to compensate for (x,y) movement, (b) segment cells, (c) extract the signals corresponding to the segmented cells from the image sequences. Motion compensation (sbxalignx & sbxaligndir) The first step that is sometimes required is to compensate for motion in the…
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positioning modes
The movement of the microscope is achieved by four motors that control the position of the objective. The motors can be independent or coupled, depending on the operating mode selected in the Position panel in the Scanbox GUI. There are three positioning modes: normal, rotated and pivot. To explain how these work, we need to define the coordinate system used…
Read MoreOnline trial averaging
It is often the case that you may want to do some quick on-line analyses on our data during the execution of an experiment. Scanbox provides a quick way to save, at the end of each experiment, the mean image during each trial. To use this feature do the following: Select “Accumulate” in the Image…
Read MoreScanbox system integration
[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…
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