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…
Read MoreNon-rigid deformation for calcium imaging frame alignment
basic 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 Morepositioning 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…
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