The Neurolabware mesoscope is up and running using our new tower system and today we took it for our first test drive with a tetO mouse. Here is the very first movie sequence of a large FOV with single-cell resolution. We can also build a panorama of a large region using Lissajous scanning (other…
Read MoreAll articles filed in scanbox
Intrinsic & epi-fluorescence imaging using the port camera
Some colleagues have asked about the possibility of integrating imaging acquisition from the port camera to do intrinsic and/or epi-fluorescence imaging ahead of targeting a region of interest with two-photon experiments in Scanbox. We have now added this option to Scanbox. To use this option you will need to wire the I2C port on the…
Read MoreSampling on a Surface
Not long ago I mentioned Scanbox’s new ability to sample on a surface. Now you can access this new feature in the GUI by navigating to the Surface Sampling panel. Surface sampling allows you to link lines of the resonant scan to depths determined by the optotune setting. In other words, it allows you to…
Read MoreTiling with Knobby
Knobby scheduler allows the user to move the microscope by specifying a list of relative changes in position at given frame numbers. One quick way to fill up the table is provided by a set of text fields in the knobby panel. This allows one to perform (x,y,z) tiling with a given range and step…
Read MoreSpatial Calibration for Multiple Objectives
Multiple users of the scope may be running projects that require different types of objectives. How to keep a spatial calibration for each and switch between them when necessary? Scanbox now includes an “objective” configuration variable — a cell array of strings each with the name of a different objective. Right now I have: Now,…
Read MoreVisualizing Individual Slices during Volumetic Imaging
During volumetric imaging, Scanbox displays all images as they are acquired. This can be inconvenient if we are trying to visually assess the activity of neurons within any one optical slice. One solution is to display the images separately in a montage by means of a Scanbox plug-in. However, it would be better to have…
Read MoreAutomatic Control of Laser Power
A new checkbox within the Laser panel (labeled AGC) allows you to turn an automatic control of laser power on and off. When AGC is on, Scanbox checks the distribution of pixel values on the image every T seconds, and increases or decreases the laser power by a certain factor if the fraction of pixels…
Read MoreAutomatic Optotune Calibration
We previously explained how to calibrate the optotune manually. With the introduction of Knobby 2, we are able to make this process automatic. You will now find a ‘Calibration’ button in the Optotune panel. To use it, do the following: Set the optotune slider to its lowest value (slide all the way down) Bring some pollen…
Read MoreA Plug-in Server
Scanbox has a memory mapped mechanism to share the incoming data stream with other processes that intend to consume the data in real-time. Examples of simple uses of such data sharing include the calculation of rolling averages, displaying a real-time histogram, or generating a montage display for volumetric data. Of course, different experiments may need…
Read MoreNew alignment and segmentation tools
Improved alignment and segmentation tools have now been released in the latest version of Scanbox, while retaining much of the functionality of the last version. sbxaligntool. The new alignment tool, shown below, adds batch processing of files, including the processing of eye and ball motion if those data are present. A region-of-interest (ROI) can optionally be…
Read More