Optogenetics with the Tower

The optogenetics panel in the new Tower electronics (aka the Pizza Box) is nearly the same as its predecessor. The main difference is that synchronization and timing of stimulation is done internally and does not require any external electronics. The parameters at the bottom specify the width of the LED, GATE pulses and the number…

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Knobby bounding box

In addition to an external limit switch, knobby implements a virtual bounding box outside of which the objective will not move. This additional safety feature is turned on by clicking the travel limit checkbox in knobby’s panel (highlighted in yellow below). The bounding box is centered on the location the objective was a the time…

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Adding a limit switch

It is desirable to have an additional safety mechanism to prevent the scope from accidentally moving beyond a certain limit, such as imposing a lower limit on the z-axis beyond which the objective might hit an object.   The firmware on the motor box can be set up so an external signal coming from a limit…

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Network streaming

The activity of segmented cells can be streamed over the network for online processing or for use in closed-loop experiments. Two configuration variables define the host name and port the data will be streamed to. In this particular example we will be streaming data to the same machine, but you can change stream_host to the…

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A Tiler Plugin

Tiler provides an example of how network commands and the plugin interface can be used together. Tiler uses network commands to move the scope to different (x,y,z) locations and to remotely change the laser power as a function of depth. It shows how to accumulate images at each site, collect the together, and save them…

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Patterned photo-stimulation for optogenetics

Scanbox allows patterned photostimulation using a dual galvo pathway.  After installation of the module he first step is to calibrate the system as follows: During installation of the galvo-galvo stimulation module, we will determine the ETL setting required to bring into alignment the 2p imaging plane and the focal plane of stimulation.  This is done…

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Event lines in Scanbox tower

Scanbox tower (aka as the PizzaBox) has 4 external TTL Event inputs on the top row of the SMA connector matrix, outlined in light blue in the picture below.   These inputs should be 5V TTL signals. Either the rising, falling or both edges of the signal can be time stamped.  This is determined by…

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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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