Scanbox

Adjusting the illumination

By: darioringach December 3, 2020

Uncategorizedepifluorescence, illumination, intrinsic imagingLeave a Comment

If you are using the port camera on the microscope to acquire intrinsic and/or epi-fluorescence imagery, it is helpful to have a tool to adjust the illumination to be even across the sample such that no regions are saturated. A new illumination checkbox is now available in the camera panel: When the camera is on,…

Achieving high frame rates with subframe folding

By: darioringach October 12, 2020

Uncategorizedfolding, frame rate, scanbox, subframe1 Comment

Scanbox samples, transfers and processes one frame at a time. Frame processing involves correcting for non-uniform spatial sampling along the resonant axis, motion stabilization, real-time extraction of signals, displaying the images, streaming to disk, and so on. This overhead in frame processing can limit the maximum frame rate achievable if the computer cannot keep up…

A Processing sketch plug-in

By: darioringach September 15, 2020September 15, 2020

M: Analysis, UncategorizedGLSL, plug-in, plugin, processing3, scanbox, two-photon imagingLeave a Comment

Processing is a versatile graphics language based on Java. Among other things, it provides a simple interface to process images using GLSL shaders. Here, I provide a simple example of a Processing sketch accessing the memory mapped data stream generated by Scanbox. This particular example simply posterizes the image using pre-defined shaders in Processing. Of…

Optogenetics with the Tower

By: darioringach February 18, 2020February 18, 2020

Uncategorizedgated PMT, optogenetics, pizza-box, scanbox, towerLeave a Comment

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…

Knobby bounding box

By: darioringach February 6, 2020February 6, 2020

Uncategorizedbounding box, configuration file, firmware, knobby, safety features, trinamicLeave a Comment

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…

Adding a limit switch

By: darioringach January 13, 2020January 14, 2020

D: Motion Control and Knobbyknobby, limit switch, motor control, position control1 Comment

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…

Network streaming

By: darioringach January 6, 2020

Uncategorizedcell segmentation, network streaming, online statistics, scanbox, Segmentation, udpLeave a Comment

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…

A Tiler Plugin

By: darioringach December 20, 2019February 6, 2020

Uncategorizednetwork, plug-in, plugin, position control, scanbox control, tilingLeave a Comment

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…

Patterned photo-stimulation for optogenetics

By: darioringach December 5, 2019December 16, 2019

N: Advanced Features, Uncategorizedgalvo-galvo, photo-stimulation, scanboxLeave a Comment

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…

Event lines in Scanbox tower

By: darioringach October 8, 2019October 8, 2019

L: External Synchronization and Controlconfiguration file, imask, synchronization, TTLsLeave a Comment

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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