Scanbox

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, scanbox1 Comment

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…

Happy Holidays from Scanbox

By: darioringach December 9, 2017

UncategorizedLeave a Comment

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…

Automatic Pockels Linearization

By: darioringach December 9, 2017January 8, 2018

H: Laser Power and Pockels Cell, Pockels Calibration and Linearization, Uncategorizedlaser power, linearization, pm100d, pockels cell, power meter, thorlabs1 Comment

Some time ago, we described a procedure to manually create a look up table for the laser power slider to achieve linear power. Now, if you have a Thorlabs’ PM100D meter your job has been made much easier, as Scanbox can perform the calibration automatically. As a first step, you will need download and install the…

Finding the optimal sample clock phase

By: darioringach November 29, 2017January 8, 2018

F: PMTs, O: Optimizations, Uncategorizedfluorescence, kraken, laser, optimal delay, phase-locked loop, PLL, scanbox, tower, two-photon5 Comments

Some time ago we talked about the advantages of synchronizing the digitizer sample clock to the laser. Our new system incorporates an on-board PLL multi-phase clock that allows Scanbox to automatically measure the contrast in a test image as a function of sample phase delay and select the optimal value for your setup. A typical measurement…

	The Mesoscope Panel… on Mesoscope features: real-time…
	The Mesoscope Panel… on Finding the optimal sample clo…
	P.T.R. Rupprecht on Synchronize to the Laser
	darioringach on Synchronize to the Laser
	P.T.R. Rupprecht on Synchronize to the Laser