Just because it is fun… This is about 4 x 3.5mm of cortex.
Read MoreAll articles filed in two photon microscope
Using the correct range and bias for PMT amplifiers
Update[6/1/2018]: Please update Scanbox to make this feature work correctly. An error in the code of earlier versions incorrectly set the gain for fixed-type amplifiers (variable type amplifiers were handled correctly). An alternative, easy way to fix the issue without having to update Scanbox is to search for the constant INPUT_RANGE_PM_1V in scanbox.m and replace…
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 MoreMeasuring 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…
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 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 MoreSimultaneous 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…
Read Morebasic 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…
Read MoreSynchronize 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…
Read MoreWelcome 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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