Scanbox

Adding a limit switch

By: darioringach January 13, 2020January 14, 2020

D: Motion Control and Knobbyknobby, limit switch, motor control, position controlLeave a 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, 2019January 13, 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…

A depth stabilization plugin

By: darioringach August 26, 2019August 27, 2019

Uncategorizedaxons, dendrites, depth, image stabilization, plug-in, plugin, scanbox, spines, stabilization, z-axis5 Comments

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,…

Using USB3 cameras with Scanbox

By: darioringach August 16, 2019

I: Behavior Monitoring, UncategorizedAllied Vision, behavior, cameras, Mako, scanbox, usb, usb3, VimbaLeave a Comment

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…

Another mesoscope movie

By: darioringach August 8, 2019August 8, 2019

Uncategorizedmesoscope, Neurolabware, two photon microscopeLeave a Comment

Just because it is fun… This is about 4 x 3.5mm of cortex.

Online, pixel-wise image processing with a Scanbox plugin

By: darioringach July 26, 2019July 26, 2019

N: Advanced Featuresorientation map, plug-in, plugin, scanbox, two-photonLeave a Comment

Sometimes you need your results right away. One example is when subsequent experiments are tailored to the properties of neurons in the population at hand. Here is a simple Scanbox plugin that computes an orientation map preference on a pixel-by-pixel basis as the data are collected. The variable mmfile.Data.header(4) indicates if a stimulus is being…

Scanbox Searches for a Population

By: darioringach July 18, 2019January 8, 2020

UncategorizedLeave a Comment

In some instances, people need to image the same population of neurons across days. It can be easy to go back to approximately the same position, but finding the best alignment can be time consuming. Now Scanbox provides a plugin that searches for the optimal location and automatically moves the microscope to the estimated position,…

	darioringach on Knobby tablet is on the Google…
	Marie on Knobby tablet is on the Google…
	Network streaming… on TTL synchronization
	A Tiler Plugin… on A Plug-in Server
	A Tiler Plugin… on Network Commands