Spatial Calibration and return to origin

We added two new features to the knobby scheduler panel, as shown below by the arrows.

knobby2nf

One (left arrow) allows knobby to perform an automatic spatial calibration of the system, measuring the (x,y) size of pixels at all magnifications.  To perform this calculation do the following:

  1. Focus on some pollen grains.  Make sure one of the pollen grains is well centered on the screen at the highest magnification (x8).
  2. Make you there is an empty folder named xx0 in the data directory you selected.
  3. Hit the calibration button (pointed by the left arrow).
  4. The system will ask you if you want to proceed.
  5. Scanbox will then loop over all magnifications, collecting data for 8 sec and moving the sample by a known distance.
  6. When it finishes, Scanbox will display the optimal value of a resonant gain magnification variable that will make your pixels square.  Note that value.

Now, when you restart Scanbox the system will read the new spatial calibration in the calibration button.  The format is [xsize ysize] [xfov yfov].  The left pair shows the width and height of a pixel (in micrometers), and the right pair shows the width and height of the field-of-view at the current magnification setting (also in micrometers).  In the example above, the (x,y) size is [0.72 0.70] um, meaning the aspect ratio is close to one.

If the aspect ratio is far from one, and you prefer square pixels, do the following:

  1. Change the value of the “gain_resonant_mult” variable in the configuration file to the one suggested by the Scanbox spatial calibration, restart Scanbox.
  2. Re-run the spatial calibration.  Thi will create a new calibration file.
  3. Restart Scanbox to read the newly created calibration file.  Now the aspect ratio should be close to one.

The second feature is one is a checkbox labeled Return. When you run a knobby schedule you have click this box to make knobby return to the initial position it started from. So, for example, upon completion of a z-stack the system will go back to where it started. Note: this feature uses the Store/Recall C function, so if you have anything stored there it will be erased.

 

 

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