New features in the volumetric scanning panel allows users to quickly populate the ETL table to perform measurements at equally spaced points. While scanning, simply move the ETL to the top of the volume you want to image and click the “Top” button to copy the location. Do the same for the bottom limit. Once…
Read MoreAll articles filed in J: Z-Scanning
Sampling 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 MoreProcessing Volumetric Data
After collecting volumetric data with the Optotune you can now process your data as follows. First, use sbxsplit() to generate separate data files for each “slice” of the optotune. For example, if I have a data file gn7_008_001.sbx collected some data with an optotune waveform having a period of 5 the command will generate a…
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 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 MoreSurface sampling in Scanbox
Answering a request from colleagues in London, the upcoming version of the Scanbox firmware will allow users to change the depth of imaging on a line-by-line basis. Up to now, during volumetric imaging, users were allowed to change the setting of the electronically tunable lens (ETL) once per frame (during the transition from one frame to another). The…
Read MoreA montage display for real-time display of volumetric data
By default, Scanbox displays the incoming image stream on its main window. Thus, during volumetric scanning, one sees the incoming images as depth is changing over time. If one is imaging only a handful of optical planes, it is difficult to see what is really going on. A different way to visualize the data in…
Read MoreCalibrating the Optotune
If you have been using the Optotune, you must have noticed that the values displayed within the optotune panel for the setting of the slider and the parameters of the z-scanning waveform are unit-less and not very useful. The latest update to Scanbox allows you to calibrate the Optotune and have all the units within the Optotune panel in micrometers.…
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 MoreFast volumetric scanning with an electrically tunable lens
We have implemented volumetric scanning in Scanbox by means of Optotune‘s electrically tunable lens, which allows for fast changes in focal plane without moving parts. Some salient features of this particular implementation are: Laser power and focus can can co-vary, allowing the brightness of the images to remain approximately constant while performing volumetric imaging. This is achieved by…
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