To enhance the real-time processing capabilities of Scanbox we now provide a general mechanism to share frames being collected with another application running concurrently on the same computer via a memory mapped file. This general and flexible mechanism allows any user to extend the real-time processing of Scanbox beyond what is already offered. As an…
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Adding an SLM path for optogenetics
As promised, there has been some progress in adding an SLM path for optogenetics to the microscope and things are looking good… We are now calling on potential users to provide input into the features that they would need/want in a GUI interface, as this may impact how useful this addition will be to our own…
Read MoreBidirectional scanning in Scanbox
We have implemented bidirectional scanning to Scanbox. To switch between bidirectional and unidirectional scanning all you have to do is hit the toggle button within the “Scanner” panel. The default setting is “U”, standing for unidirectional scanning; hitting the button will switch it to “B”, indicating bidirectional scanning. You can only switch between the two modes while the…
Read MoreReal-time, motion compensation in Scanbox
Our colleague Tobias Rose was recently asking about Scanbox’s ability to stabilize the motion of images and signals from regions-of-intrest (ROIs) in real-time. The goal of such processing is to be able to do experiments in closed-loop, and do very quick analyses on the neuronal responses, such as computing tuning curves on the fly. Below is a…
Read MoreReal-time signal extraction, visualization and processing in scanbox 2.0
Here is a sneak preview of the new features to be released with Scanbox 2.0. Some of the salient additions include: Automatic stabilization: The system can automatically correct for rigid (x,y) translation in real time. Selection of regions of interest (ROIs): Allows for the selection of regions of interest that need to be tracked in real-time. After their definition,…
Read Morebasic processing pipeline
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…
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…
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 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…
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