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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Using an auxiliary USB DAQ to sample TTL events

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…

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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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Mesoscope features: real-time panoramas, ROI selection, zoom/pan, and dynamic ROIs

Here are some of the features we have been developing to make it easy to build panoramas, pick regions-of-interest, and to visualize ROI location and data during acquisition using the NLW Mesoscope (aka the Kraken) on the latest version of Scanbox. The video below shows a brief demo of the following: The automatic creation of…

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Finding the optimal sample clock phase

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…

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Using the correct range and bias for PMT amplifiers

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…

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Taking the mesoscope for a test drive

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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Intrinsic & epi-fluorescence imaging using the port camera

Some colleagues have asked about the possibility of integrating imaging acquisition from the port camera to do intrinsic and/or epi-fluorescence imaging ahead of targeting a region of interest with two-photon experiments in Scanbox. We have now added this option to Scanbox. To use this  option you will need to wire the I2C port on the…

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