The following explains how to connect GigE cameras to your Scanbox. If you have trouble following the instructions below just let me know — I can help remotely. ScanBox has the ability to acquire images from cameras synchronized to the frames of the microscope. We typically use one camera to monitor eye movements and a second one to monitor…
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Scanbox gets a github repository
As a way to streamline all future updates to Scanbox, to report and resolve issues, and to develop a Wiki for documentation and discussions, I created a Github repository for Scanbox. This is a private repository for users of Scanbox. If are already a Scanbox user, please open a GitHub account and email me your username, so…
Read MoreUsing auto-stabilization
Real-time auto-stabilization in Scanbox Yeti is achieved by tracking the displacement of 2D features in a number of small windows relative to a reference image. We prefer tracking cells within a handful of small windows because slow gradients in the image can easily bias the resulting estimates for large regions. Here are some step-by-step instructions on how…
Read MoreBlack label, limited edition, Scanbox controller
The black label, limited edition, vastly improved, Scanbox controller arrived! Coming soon to a microscope near you…
Read MoreScanbox Yeti (beta) has arrived!
Scanbox Yeti is here! Why Yeti? I don’t really know… but it sounds nice. Future versions will take the names of other mythical creatures as well. We should credit Josh Trachtenberg for this intellectual contribution to the project. We have been using Scanbox Yeti in the Lab for about a month without major problems and we…
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 MoreSorting calcium imaging signals
Real-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 MoreReading raw data with sbxread()
Raw image data in scanbox is contained in *.sbx files. To read these data you can use the sbxread() function. Here is the documentation from its help section– So, for example, the following lines of code will read images from 0 to 19 (20 total) and display the average of the first (green) PMT channel: And you may…
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