Using the correct range and bias for PMT amplifiers

You may have one of two different PMT amplifiers in your setup.  One which has a variable gain. The typical settings of this amplifier should be: left the switch on GND, middle switch on L or H but with the knob set to a gain of 10^4, next switch on FBW and DC for the…

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New 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…

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Measuring the field of view and validating the uniformity of spatial correction

If you followed the instructions on spatial calibration you should have a nice uniform field in Scanbox.  One simple way to measure the resulting spatial resolution and spatial uniformity at each zoom setting is to mount a 40 line pairs per mm RONCHI calibration slide on top of a green aut0-fluorescent slide.  By aligning the…

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Bidirectional 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…

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Quick 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…

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Simultaneous control of an electrically tunable lens and a pockels cell

We are preparing Scanbox for fast, volumetric scanning, by providing simultaneous control of an electrically tunable lens (to focus on different planes) and a Pockels cell (to control laser power). The Scanbox card has an integrated, 12-bit current source used to control the focus tunable lens. Similarly, an integrated DAC on the Scanbox card controls laser power via a Pockels cell. The…

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basic processing pipeline

Scanbox includes some basic processing functions that you can use to (a) align the images to compensate for (x,y) movement, (b) segment cells, (c) extract the signals corresponding to the segmented cells from the image sequences. Motion compensation (sbxalignx & sbxaligndir) The first step that is sometimes required is to compensate for motion in the…

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Synchronize to the Laser

Scanbox makes sure the data acquisition of the signals from the photo-multipliers are synchronized to the laser pulse.  Let me explain why.  Suppose you run an asynchronous data acquisition clock at 25Mhz while the laser has a pulse rate of 80Mhz.  Then you may obtain images of single cells that look like this: This is…

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Welcome to Scanbox!

Welcome to Scanbox File Exchange.  This is a site where you can find regular updates to the scanbox software for two-photon imaging, report bugs, share data analysis tools and ideas for improvement. As time goes by we will be posting tips and tricks on how to use the software, insights into the code (the Matlab…

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