kraken

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)

Capture

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.

 

 

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 showing the change in normalized contrast of a target image as a function of phase delay (here the range from -8 to 8 covers the entire 12.5 ns period of the laser).

pll_1

Scanbox automatically shows the resulting images, on the same scale, for each phase delay value as well:

pll2

Scanbox will also plot the normalized images obtained for the settings that yield the lowest and and highest contrasts:

pll_best_worse

One can clearly see from the images that phase does not simply scale the contrasts of the images, but has an obvious effect on their SNR.  (Why this occurs exactly is still a matter of debate here, but data rule and the results are clear.)

This option will be automatically available to those who adopt the new tower system.  What can you do if you have one of the older systems?  You can simply change the sample clock phase by extending the length of the cable running from the laser SYNC OUT to the external clock of the digitizer.  Extensions of 50cm in length can be connected together to yield phase steps of 1/8th of the laser period.  So if you want to optimize the contrast and SNR of your images take a day off to find your optimal delay and improve the quality of your data.

Bada boom! New system coming soon!

So why the long silence in the Scanbox blog?

We have been working hard on a the development of our new system. A modular, expandable system that will run the new line of Neurolabware microscopes (aka the Kraken microscope) and is backward compatible with our previous box.

Want a sneak peak?

Bada boom!

 

nlw-full-tower

Here is a closeup of some of the LCD/power modules…

nlw-lcd-module

nlw-pwr-open

If you are interested in the new features of the Kraken microscope and the new modular system please get in touch with Neurolabware.