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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Support for Phenosys Speedbelt Linear Treadmill

Scanbox now provides a direct interface to Phenosys’ speedbelt.  Once the speedbelt is connected via the USB to the computer it will show up as a COM port on the Device Manager.  To acquire input from the treadmill, simply define the speedbelt_com configuration variable specifying the corresponding COM port. Within the Scanbox “Treadmill and Encoder”…

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Motor box update

We are asking all Scanbox users to update to the latest version of Scanbox which incorporates important updates to the motor box code, including: Update of the Trinamic firmware Update of the motor box application code Update of the motor box interface code in Scanbox Please proceed as follows: If you don’t have the Trinamic…

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Happy Holidays from Scanbox

Happy holidays to all Scanbox users! This was a very productive year.  We introduced a number of new features including: Introduction of Virtual Knobby Introduction of Knobby 2.0 Introduction of Knobby Scheduler Support for TTL start/stop acquisition mode Enhancements to alignment and segmentation tools Introduction of the plugin server Introduced spatial calibration and return to origin…

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