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…

Read More

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…

Read More

External TTL trigger

To automatically start /stop acquisition by means of an external TTL signal follow the following instructions. First, connect an appropriate TTL control signal to the P1.6 (pin #21) of the extension header of the Scanbox board.  The view below shows a top view of the Scanbox control board.  The pin in question is located on…

Read More

Simultaneous imaging and electrophysiology

Scanbox now allows the possibility of doing simultaneous imaging and electrophysiology.  An external DAQ device, supported by Matlab’s data acquisition toolbox, is need to do this.  In our case, we had an old NI-USB-6221 lying around that we decided to use. In the present case, we set things up to do patch-clamp recordings from a single…

Read More

TTL synchronization

The simplest way to synchronize external stimulation with the microscope data collection is for the user to generate a TTL signal that is HIGH when the stimulus is on and LOW when it is off. This signal should be split and connected to the TTL1 input of Scanbox and the AUX1 input of the Alazartech card…

Read More

Using the quadrature encoder to track locomotion

Scanbox allows you to acquire the position of a rotating platform at each frame of the microscope.  To do so, you need a quadrature encoder to be mounted on the axis of your platform.  We use the US Digital HS-360-IE-S, but any quadrature encoder will do as well. The encoder needs to be wired to an Arduino…

Read More

Blanking the laser between trials

Sometimes, during long behavioral sessions, it is advantageous to turn off the laser between trials to minimize damage while keeping the microscope scanning.  To do this without introducing any additional noise that may influence the behavioral state we use the Pockels cell.  Scanbox now allows one to blank the laser by sending a command over…

Read More

Scanbox system integration

[Updated Dec 2015] Integrating a Scanbox-controlled microscope with your system rather pretty straightforward after you understand how the system samples external events and how it can be controlled over the network. Monitoring external TTL events When Scanbox runs it monitors external events on its TTL inputs.  Two TTL inputs, labeled TTL0 and TTL1, are readily available as SMA…

Read More