Scanbox allows patterned photostimulation using a dual galvo pathway. After installation of the module he first step is to calibrate the system as follows: During installation of the galvo-galvo stimulation module, we will determine the ETL setting required to bring into alignment the 2p imaging plane and the focal plane of stimulation. This is done…
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Online, pixel-wise image processing with a Scanbox plugin
Sometimes you need your results right away. One example is when subsequent experiments are tailored to the properties of neurons in the population at hand. Here is a simple Scanbox plugin that computes an orientation map preference on a pixel-by-pixel basis as the data are collected. The variable mmfile.Data.header(4) indicates if a stimulus is being…
Read MoreSimultaneous imaging with port and behavior cameras
If you have one of the new systems (aka as the pizza box) you can now acquire imagery simultaneously from the port camera and the behavior cameras. During 2p imaging the behavior cameras are triggered at the beginning of a frame (TTL OUT 1x f.r.) or at the beginning and middle of a frame (TTL…
Read MoreOptogenetics with Scanbox
The latest version of Scanbox includes a panel to allow uses to perform 1p optogenetics with 2p imaging. The panel provides an interface to the ThorLabs DC2200 dual channel controller, but can also be used with the simpler T-cube driver. You can use the LED of your preference. We have been working both with mounted…
Read MoreVisualizing Individual Slices during Volumetic Imaging
During volumetric imaging, Scanbox displays all images as they are acquired. This can be inconvenient if we are trying to visually assess the activity of neurons within any one optical slice. One solution is to display the images separately in a montage by means of a Scanbox plug-in. However, it would be better to have…
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 MoreA rolling average plug-in for scanbox
Scanbox offers a memory-mapped interface mechanism to expose incoming data to other processes. This facilitates a wide rage of customization by users that may want to display their data in different ways or do some on-line processing not currently supported by Scanbox. We previously provided one example of how a real-time histogram of the data can…
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 MoreMemory-mapped data-sharing for real-time processing
To enhance the real-time processing capabilities of Scanbox we now provide a general mechanism to share frames being collected with another application running concurrently on the same computer via a memory mapped file. This general and flexible mechanism allows any user to extend the real-time processing of Scanbox beyond what is already offered. As an…
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