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…
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Processing 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 MoreBidirectional scanning and resonant driver calibration
Resonant mirrors vary somewhat in their resonant frequency and the settings of the mirror controller must be adjusted to obtain the best possible images in bidirectional mode. A synchronization signal from the resonant board must be adjusted so that it is both symmetric and its phase is aligned with the zero crossings of the mirror…
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.…
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