A 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…

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Optogenetics with the Tower

The optogenetics panel in the new Tower electronics (aka the Pizza Box) is nearly the same as its predecessor. The main difference is that synchronization and timing of stimulation is done internally and does not require any external electronics. The parameters at the bottom specify the width of the LED, GATE pulses and the number…

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Network streaming

The activity of segmented cells can be streamed over the network for online processing or for use in closed-loop experiments. Two configuration variables define the host name and port the data will be streamed to. In this particular example we will be streaming data to the same machine, but you can change stream_host to the…

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Patterned photo-stimulation for optogenetics

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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A depth stabilization plugin

Some experiments require long imaging times. In cases where we are recording from  small structures, such as dendritic processes or spines, any slow drift in the depth of the imaging plane would affect the quality of the data. Here is a Scanbox plugin that will: (a) perform a quick z-stack around the desired imaging plane,…

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Using USB3 cameras with Scanbox

Scanbox has long supported the use of GigE cameras for behavior, but integrating USB3 cameras which support an external trigger is also possible.  As an example, consider the Mako-U series. Wire up the camera To use one of these cameras you have to be using a trigger cable.  Different manufacturers offer cables that differ in…

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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…

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Improved 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…

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Using Suite2p with Scanbox

Marius Pachitariu and Carsen Stringer released a Python version of their Suite2p pipeline for two-photon imaging. So I decided to take this tool for a test drive with data collected from Scanbox. At the moment, Suite2p takes tiff and hdf5 files, so we first decided to write a function to convert *.sbx to *.h5 files. …

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Optogenetics 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…

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