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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A Tiler Plugin

Tiler provides an example of how network commands and the plugin interface can be used together. Tiler uses network commands to move the scope to different (x,y,z) locations and to remotely change the laser power as a function of depth. It shows how to accumulate images at each site, collect the together, and save them…

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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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Scanbox Searches for a Population

In some instances, people need to image the same population of neurons across days.   It can be easy to go back to approximately the same position, but finding the best alignment can be time consuming. Now Scanbox provides a plugin that searches for the optimal location and automatically moves the microscope to the estimated position,…

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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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Network Commands

The basics of how to control the microscope over the network have been described here. Over time, a number of other commands have been added to facilitate the control of Scanbox remotely.  Here is an up-to-date list of network commands.  If there are others you need just let us know. File storage: A<string> Set animal…

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