With the ability to read Scanbox binaries in Suite2p I wrote a one-line processing pipe-line for Scanbox. If you are within a data directory with folders you want to process, all you have to is pass a list of the experiments to sbxsuite2p(): This example just contains a list of two experiments. Matlab will then…
Read MoreAll articles filed in two-photon imaging
Real-time imaging and pose estimation
I’ve made substantial progress to read real-time DeepLabCut Live date (see paper by Kane et al here) from Scanbox. As you can see in the example below, I got to the point where we can do two-photon imaging and pose estimation in real time. As you recall, the behavior cameras in Scanbox are triggered once…
Read MoreA Processing sketch plug-in
Processing is a versatile graphics language based on Java. Among other things, it provides a simple interface to process images using GLSL shaders. Here, I provide a simple example of a Processing sketch accessing the memory mapped data stream generated by Scanbox. This particular example simply posterizes the image using pre-defined shaders in Processing. Of…
Read MoreImproved adjustment of ROIs location, laser power and depth in the mesoscope
We have made some recent improvements to the mesoscope GUI (thanks to Zaneta Navratilova and Dhruba Banerjee from Bruce McNaughton Lab at UCI for the feedback). The new interface allows users to: Quickly create a wide-field panorama Define ROIs and their locations Adjust the depth (ETL setting) and laser power for each ROI. Save/Load previously…
Read MoreAutomatic Control of Laser Power
A new checkbox within the Laser panel (labeled AGC) allows you to turn an automatic control of laser power on and off. When AGC is on, Scanbox checks the distribution of pixel values on the image every T seconds, and increases or decreases the laser power by a certain factor if the fraction of pixels…
Read MoreA Plug-in Server
Scanbox has a memory mapped mechanism to share the incoming data stream with other processes that intend to consume the data in real-time. Examples of simple uses of such data sharing include the calculation of rolling averages, displaying a real-time histogram, or generating a montage display for volumetric data. Of course, different experiments may need…
Read MoreScanbox and me on a boring afternoon
What do you do on a boring afternoon with a two-photon microscope? Looking at small stuff of course! All these guys are from the Carolina mixed pollen grains slide.
Read MoreLatest Scanbox Release brings cool performance improvements
The latest Scanbox release brings a major performance improvement. The main bottleneck in the acquisition loop consists of a function that re-arranges the incoming pixel stream into the images that are displayed and stored in real-time. This function now makes use of OpenMP to distribute the work among different physical cores available in your machine…
Read MoreA 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 MoreInstalling knobby
Many of you will be receiving Knobby in the mail soon. Installing it is easy. Just follow these steps: Connect knobby to a USB port Open the Device Manager and check which COM port # knobby was assigned to (it is the one displaying an Arduino Due board). Open Matlab, edit scanbox_config.m and set the…
Read More
Scanbox 