Scanbox

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-photon4 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…

Using the correct range and bias for PMT amplifiers

By: darioringach November 28, 2017June 2, 2018

F: PMTs, O: Optimizations, Uncategorizedpmt amplifier, scanbox, transimpedance, two photon microscope3 Comments

Update[6/1/2018]: Please update Scanbox to make this feature work correctly. An error in the code of earlier versions incorrectly set the gain for fixed-type amplifiers (variable type amplifiers were handled correctly). An alternative, easy way to fix the issue without having to update Scanbox is to search for the constant INPUT_RANGE_PM_1V in scanbox.m and replace…

Taking the mesoscope for a test drive

By: darioringach October 24, 2017October 25, 2017

Uncategorizedgolem, mesoscope, scanbox, tower system, wide field of viewLeave a Comment

The Neurolabware mesoscope is up and running using our new tower system and today we took it for our first test drive with a tetO mouse. Here is the very first movie sequence of a large FOV with single-cell resolution. We can also build a panorama of a large region using Lissajous scanning (other…

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