By default, Scanbox displays the incoming image stream on its main window. Thus, during volumetric scanning, one sees the incoming images as depth is changing over time. If one is imaging only a handful of optical planes, it is difficult to see what is really going on. A different way to visualize the data in…
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A plug-in for real-time histograms in Scanbox
A Scanbox user requested to add the ability to display a histogram of image values in real-time. Here, I use a the general mechanism of memory mapped files in Scanbox to show how easy is to add such “plug-ins” to provide additional functionality to the system. The Matlab code necessary to add real-time histograms in Scanbox is…
Read MoreNon-rigid image alignment in twenty lines of Matlab
We have previously discussed rigid and non-rigid image alignment algorithms for calcium imaging data. If you have the image processing toolbox, a particularly compact solution for non-rigid image registration can be written in ~20 lines of code or so. The code below returns a displacement field for each frame in the image sequence (output variable ‘disp’) that needs…
Read MoreSimultaneous imaging and electrophysiology
Scanbox now allows the possibility of doing simultaneous imaging and electrophysiology. An external DAQ device, supported by Matlab’s data acquisition toolbox, is need to do this. In our case, we had an old NI-USB-6221 lying around that we decided to use. In the present case, we set things up to do patch-clamp recordings from a single…
Read Moreauto-tuning bidirectional scanning
To properly align even and odd lines in bidirectional tuning one has to set the values of the configuration variable ‘ncolbi’. This variable is a vector where each entry controls how lines are ‘folded’ for each of the magnification settings, x1, x2 and x4. The latest version of scanbox includes a function sbxautocalbd() that allows you to automatically determine the…
Read MoreScanbox 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 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…
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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Scanbox 