Motor box update

We are asking all Scanbox users to update to the latest version of Scanbox which incorporates important updates to the motor box code, including: Update of the Trinamic firmware Update of the motor box application code Update of the motor box interface code in Scanbox Please proceed as follows: If you don’t have the Trinamic…

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Happy Holidays from Scanbox

Happy holidays to all Scanbox users! This was a very productive year.  We introduced a number of new features including: Introduction of Virtual Knobby Introduction of Knobby 2.0 Introduction of Knobby Scheduler Support for TTL start/stop acquisition mode Enhancements to alignment and segmentation tools Introduction of the plugin server Introduced spatial calibration and return to origin…

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Automatic Pockels Linearization

Some time ago, we described a procedure to manually create a look up table for the laser power slider to achieve linear power.  Now, if you have a Thorlabs’ PM100D meter your job has been made much easier, as Scanbox can perform the calibration automatically. As a first step, you will need download and install the…

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Finding the optimal sample clock phase

Some time ago we talked about the advantages of synchronizing the digitizer sample clock to the laser.  Our new system incorporates an on-board PLL multi-phase clock that allows Scanbox to automatically measure the contrast in a test image as a function of sample phase delay and select the optimal value for your setup. A typical measurement…

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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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Taking the mesoscope for a test drive

The Neurolabware mesoscope is up and running using our new tower system and today we took it for our first test drive with a tetO mouse. Here is the very first movie sequence of a large FOV with single-cell resolution.   We can also build a panorama of a large region using Lissajous scanning (other…

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Intrinsic & epi-fluorescence imaging using the port camera

Some colleagues have asked about the possibility of integrating imaging acquisition from the port camera to do intrinsic and/or epi-fluorescence imaging ahead of targeting a region of interest with two-photon experiments in Scanbox. We have now added this option to Scanbox. To use this  option you will need to wire the I2C port on the…

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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…

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Tiling with Knobby

Knobby scheduler allows the user to move the microscope by specifying a list of relative changes in position at given frame numbers.  One quick way to fill up the table is provided by a set of text fields in the knobby panel.  This allows one to perform (x,y,z) tiling with a given range and step…

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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…

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