The first image acquired by Yeti is just 1 year old! Happy birthday Yeti! We have seen Yeti grow a lot during the first year…. He added capabilities to stabilize images and extract signals in real-time, enlarged the field of view, offered volumetric scanning allowing for co-variation of laser power and focal plane, included bidirectional scanning, provided on-line computer-assisted segmentation, linear power…
Read MoreBlanking the laser between trials
Sometimes, during long behavioral sessions, it is advantageous to turn off the laser between trials to minimize damage while keeping the microscope scanning. To do this without introducing any additional noise that may influence the behavioral state we use the Pockels cell. Scanbox now allows one to blank the laser by sending a command over…
Read MoreScanbox is Windows 10 compatible
We have upgraded to Windows 10 without major problems. Scanbox along with all the other drivers appear to be running just fine. The only issue that we ran into is access to the parallel computing toolbox using a GeForce GTX Titan Z card. While Scanbox can still run without the parallel computing toolbox, some features will be…
Read Moreauto-tuning bidirectional scanning
To properly align even and odd lines in bidirectional tuning one has to set the values of the configuration variable ‘ncolbi’. This variable is a vector where each entry controls how lines are ‘folded’ for each of the magnification settings, x1, x2 and x4. The latest version of scanbox includes a function sbxautocalbd() that allows you to automatically determine the…
Read MoreLinear power
The following procedure will allow you to define a linearization table for your Pockels’ cell so you can obtain a linear power change with equal steps in the value of the power slider in Scanbox. During imaging the laser power is controlled by an 8-bit DAC that ranges from from 0V (at a DAC register value…
Read MoreHow large can you go?
Following the recent post on expanding the field of view, Cris Neill sends us a beautiful movie of an imaging field of 1.2 x 1.2 mm. How large can you go?
Read MoreLarger field of view and finer control of pixel size
There have been requests for Scanbox to accommodate a larger field of view and the ability to precisely calibrate the aspect ratio and size of pixels. The latest version (along with modifications in the firmware) allow you to do just this. [This paragraph about the diodes is only relevant to older boards] A first step to maximize…
Read MoreOnline cell segmentation in Scanbox
There is one hidden feature of Scanbox that has been around for some time, but I have not yet described. This feature allows for computer-assisted segmentation during an experiment. As you must already know, one way in which region of interests (ROIs) can be defined is manually. This process can be initiated by clicking on the Add button…
Read MoreQuick start guide to the Optotune and volumetric scanning
Scanbox uses an on-board current source to control the Optotune lens, so that changes in depth are synchronized to the beginning of each microscope frame. Once the lens is installed, the easiest way to verify its function is to start imaging a sample and move the slider in the Optotune panel to change the plane of…
Read MoreVisualizing Scanbox stacks with Vaa3D
Some scanbox functions allow you to export *.sbx files to *.tif files that can be then visualized using other software like Vaa3d or ImageJ. For example, after collecting a z-stack you can use sbxtifstack() to generate a tif file that can be read directly using Vaa3d. If your stack has the hypothetical file name abc_010_nnn.sbx…
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