Scanbox

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-axis4 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, 2019

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,…

Simultaneous imaging with port and behavior cameras

By: darioringach July 11, 2019July 29, 2019

E: Camera Port, I: Behavior Monitoring, N: Advanced Featuresbehavior, epifluorescence, intrinsic imagingLeave a Comment

If you have one of the new systems (aka as the pizza box) you can now acquire imagery simultaneously from the port camera and the behavior cameras. During 2p imaging the behavior cameras are triggered at the beginning of a frame (TTL OUT 1x f.r.) or at the beginning and middle of a frame (TTL…

Improved adjustment of ROIs location, laser power and depth in the mesoscope

By: darioringach March 7, 2019March 9, 2019

mesoscopedynamic ROIs, mesoscope, region of interest, scanbox, two-photon imagingLeave a Comment

We have made some recent improvements to the mesoscope GUI (thanks to Zaneta Navratilova and Dhruba Banerjee from Bruce McNaughton Lab at UCI for the feedback). The new interface allows users to: Quickly create a wide-field panorama Define ROIs and their locations Adjust the depth (ETL setting) and laser power for each ROI. Save/Load previously…

The Mesoscope Panel

By: darioringach August 31, 2018

A: Quick Startbrain, field of view, FOV, imaging, mesoscope, ROIs, two-photonLeave a Comment

If you are already familiar with Scanbox on the NLW standard system, you will find it very natural to use the new options available in the mesoscope. When Scanbox is configured to operate the mesoscope, you will find a new panel giving access to the features that go beyond those of the standard configuration: Here is…

Using Suite2p with Scanbox

By: darioringach August 29, 2018

Alignment, Segmentation, UncategorizedCarsen Stringer, Marius Pachitariu, pipeline, Python, scanbox, suite2p, two-photonLeave a Comment

Marius Pachitariu and Carsen Stringer released a Python version of their Suite2p pipeline for two-photon imaging. So I decided to take this tool for a test drive with data collected from Scanbox. At the moment, Suite2p takes tiff and hdf5 files, so we first decided to write a function to convert *.sbx to *.h5 files. …

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