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 MoreAll articles filed in March 2014
Recursive 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…
Read MoreThe Heart of Scanbox
The heart of Scanbox is the custom designed card shown below, now in its third revision: Here is a brief summary of the architecture. The card communicates with the host PC through a USB line. A number of Matlab functions allows one to easily communicate with the card, sending scanning parameters, starting and stopping scanning,…
Read MoreA Quick Look at Scanbox’s GUI
In case you were wondering, this is how things look for now in the first release of Scanbox 1.0. Click on the figure to get a larger picture. Here is a brief description of the panels. Chameleon: it allow you to change the laser wavelength, power and read out the laser status. Scanner: Defines scanning parameters including the…
Read MoreWelcome to Scanbox!
Welcome to Scanbox File Exchange. This is a site where you can find regular updates to the scanbox software for two-photon imaging, report bugs, share data analysis tools and ideas for improvement. As time goes by we will be posting tips and tricks on how to use the software, insights into the code (the Matlab…
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