Month: December 2017

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:

  1. Update of the Trinamic firmware
  2. Update of the motor box application code
  3. Update of the motor box interface code in Scanbox

Please proceed as follows:

  • If you don’t have the Trinamic IDE 3.0 installed, please download and install it.
  • After you launch the IDE select Tools->Firmware update from the menu.
  • Under “select firmware” select $SCANBOX/trinamic/TMCM-6110_V142.hex, where $SCANBOX is the root directory for the latest Scanbox distribution you downloaded
  • Click the update button


  • Close the Firmware update window
  • Click on the TMCL creator entry on the left column; the Editor will pop up
  • Do File->Open and select $SCANBOX/scanknob/scanknob_v3.tmc
  • Click the download button highlighted in blue below.


  • Answer the questions that come up in the panels in the positive. In the end, you will see a message saying the code was downloaded successfully.
  • Follow the remaining set of instructions on how to update Scanbox, skipping the line that asks you to update the firmware in the motor box.

Please note

  • The new Trinamic application firmware (scanknob_v3.tmc) includes a piece of code that will prevent you from moving down in the Z-axis too quickly.  So, if you start spinning the Z knob to go down, the box will go into panic mode and freeze all motors.  If this happens knobby will become unresponsive and you need to restart Scanbox to unlock it.
  • If you prefer not to have this feature installed, simply install the previous version (scanknob_v2.tmc) instead
  • Before you go back to imaging, please remove the objective from the scope, start-up Scanbox, and make sure all axes are moving as expected. Image some pollen grains and make sure all is working as expected.  Only after checking everything appears to be working fine, go back to imaging.
  • As you perform these tests, make sure you have rapid access to the motor box power switch so you can turn it off quickly if there is such a need.
  • If, after this update, your z-motor appears to jitter as you move, revert to the scanknob_v2.tmc firmware.


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 with Knobby 2.0
Developed remote control of microscope position with click-and-center mode
Developed automatic calibration of the optotune
Introduced automatic gain control of laser power
Support for visualization of individual slices during acquisition of volumetric data
Support of spatial calibration for multiple objectives
Introduced new functions to process volumetric data
Developed tiling with Knobby 2.0
Introduced methods to program ETL to sample on a surface
Support of intrinsic and wide-field imaging
Added configuration settings for different PMT amplifiers
Developed PPL delay line for optimal sample clock phase
Introduced support for the NLW Mesoscope
Developed automatic procedure for pockels cell calibration
Completed development of our new tower system

All software features are offered at no additional cost to our Scanbox users.

What will 2018 bring?

Well… that depends on your requests for new features. What do you like to see implemented?  What needs improvement?

Let us know in the comments below!


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 software for the PM100D.

Connect the power meter to the computer with an USB cable and start up Matlab.  If you launch the Test and Measurement Tool (tmtool) you should see the instrument listed under VISA | USB as shown in the figure below.


Make a note of the identification string.  Edit scanbox_config and set the variable ‘pmeter_id’ to this ID string. In the present example, we would have a line that reads:

sbconfig.pmeter_id = 'USB0::0x1313::0x8078::P0012223::0::INSTR'; % PM100D power meter ID (leave blank if not available)

Launch Scanbox and scroll through the different panels.  You should now see a panel labeled Power Meter and, within the panel there is a button labeled Calibration.

To use the calibration tool place the sensor of the PM100D at the output of the pockels cell.  Make sure the bias of the pockels controller is set so you get minimum power when Scanbox is not scanning.  Now, make sure the laser shutter is open.  You can now hit the Calibration button, sit back and relax.

Scanbox will start changing the DAC values and reading the power at each setting.  A graph will be plotted online as the process takes place.  At the end you will get a graph that looks like this:



The blue dots show the raw data, while the red line is a fit to the points which is used to compute the linearization table.

Immediately after the look up table is computed, Scanbox will perform a validation step, measuring the power at the different settings after installing the new lookup table. Once the measurements are complete, you should get a pretty linear graph, like this:


Scanbox saves the resulting linearization table in pockelscal.mat, so next time you start Scanbox that lookup table will be automatically loaded (overriding whatever settings you have in the configuration file).

That’s it! (Remember to take the sensor out of the path when you are done!)

Mesoscope features: real-time panoramas, ROI selection, zoom/pan, and dynamic ROIs

Here are some of the features we have been developing to make it easy to build panoramas, pick regions-of-interest, and to visualize ROI location and data during acquisition using the NLW Mesoscope (aka the Kraken) on the latest version of Scanbox.

The video below shows a brief demo of the following:

  1. The automatic creation of panoramas on-the-fly as data are collected.
  2. Selection of region-of-interests (ROIs) directly on the panorama view.
  3. Visualizing ROI data embedded in the panorama.
  4. Dynamically zooming and panning during data collection.
  5. Dynamically changing the location of ROIs by dragging them on the panorama during the collection of data.

Here are some raw data from two separate ROIs, one on each hemisphere.

The ROIs (full panorama FOV in this example is 4.0 x 3.5 mm)


And a short movie with raw data:

Thinking about getting a mesoscope?  Add your wish list of features in the comments below.  Better now than later, as some features can dictate design considerations.