Scanbox

Scanbox Searches for a Population

By: darioringach July 18, 2019

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,…

Simultaneous imaging with port and behavior cameras

By: darioringach July 11, 2019July 12, 2019

E: Camera Port, I: Behavior Monitoring, N: Advanced Featuresbehavior, epifluorescence, intrinsic imagingLeave a Comment

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…

Improved adjustment of ROIs location, laser power and depth in the mesoscope

By: darioringach March 7, 2019March 9, 2019

mesoscopedynamic ROIs, mesoscope, region of interest, scanbox, two-photon imagingLeave a Comment

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…

The Mesoscope Panel

By: darioringach August 31, 2018

A: Quick Startbrain, field of view, FOV, imaging, mesoscope, ROIs, two-photonLeave a Comment

If you are already familiar with Scanbox on the NLW standard system, you will find it very natural to use the new options available in the mesoscope. When Scanbox is configured to operate the mesoscope, you will find a new panel giving access to the features that go beyond those of the standard configuration: Here is…

Using Suite2p with Scanbox

By: darioringach August 29, 2018

Alignment, Segmentation, UncategorizedCarsen Stringer, Marius Pachitariu, pipeline, Python, scanbox, suite2p, two-photonLeave a Comment

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. …

Optogenetics with Scanbox

By: darioringach May 23, 2018

F: PMTs, N: Advanced Features, Uncategorizedarduino, gated PMT, Hamamatsu, optogenetics, scanboxLeave a Comment

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…

Network Commands

By: darioringach March 28, 2018May 23, 2018

A: Quick Start, L: External Synchronization and Control, Uncategorizedcontrol, network, protocol, scanbox2 Comments

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…

Using an auxiliary USB DAQ to sample TTL events

By: darioringach March 21, 2018

L: External Synchronization and Controlbuffering, external TTLs, NI-DAQ, scanboxLeave a Comment

We have added an option to sample an additional 8 TTL inputs from Scanbox using an external NI DAQ device. In our case, we have used and tested the NI USB-6221, but any other devices which support sampled, digital IO should work as well. The configuration file now contains four lines that specifies the parameters…

Support for Phenosys Speedbelt Linear Treadmill

By: darioringach March 5, 2018March 5, 2018

Behavior Data, Uncategorizedphenosys, scanbox, speedbelt, treadmill, two-photonLeave a Comment

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”…

Motor box update

By: darioringach December 13, 2017January 8, 2018

D: Motion Control and Knobby, Uncategorizedmotor box, motor control, scanbox, trinamicLeave a Comment

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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