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…
Read MoreAnother mesoscope movie
Just because it is fun… This is about 4 x 3.5mm of cortex.
Read MoreOnline, pixel-wise image processing with a Scanbox plugin
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…
Read MoreScanbox Searches for a Population
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,…
Read MoreSimultaneous imaging with port and behavior cameras
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…
Read MoreImproved adjustment of ROIs location, laser power and depth in the mesoscope
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…
Read MoreThe Mesoscope Panel
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…
Read MoreUsing Suite2p with Scanbox
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. …
Read MoreOptogenetics with Scanbox
The latest version of Scanbox includes a panel to allow uses to perform 1p optogenetics with 2p imaging. The panel provides an interface to the ThorLabs DC2200 dual channel controller, but can also be used with the simpler T-cube driver. You can use the LED of your preference. We have been working both with mounted…
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