Pixel Size Calibration

As a central feature for virtually all imaging, specifying a pixel's physical dimensions is handled within µManager:


 * 1) First, we need to actually determine the pixel size.
 * 2) Load a sample into the system. Beads may be easiest, though anything with well-defined features will do.
 * 3) Using the motor navigation in µManager's Live Window, locate any such feature.
 * 4) Using Fiji's magnification tool, zoom in to allow for precise placement of a ROI.
 * 5) Using the line ROI tool, drag a line from a recognizable point on the future to the right (its precise endpoint will be moved momentarily).
 * 6) Press the left arrow key. This will instruct µManager to move the stage by 10 steps.
 * 7) While moving the endpoint of the line ROI to the new location of the feature, pay attention to Fiji's status bar: it displays the current length of the line.
 * 8) Once the line is spanning the distance the feature moved, record this distance as X pixels.
 * 9) The value to use for your pixel size will be (10 motor steps) / (X pixels). (The observant will note that this is not, in fact, in pixels/µm (unless the stage moves in precisely 1 µm steps). As of OpenSPIM 1.0, the motor locations are displayed and manipulated in motor steps rather than µm; as a result, although the units are incorrect, the behavior is as desired.)
 * 10) Now we'll enter the value into µManager's configuration. Click Tools -> Pixel Size calibration
 * 11) The OpenSPIM plugin will have automatically provided a 'calibration' called (descriptively) "Uncalibrated" which sets a pixel to be 1 µm. This is to ensure that µManager's built-in Live Window panning (which requires an active pixel size calibration) works with minimal configuration. Select it, then click Edit.
 * 12) Re-labelling the configuration will help identify it, but isn't required.
 * 13) In the window that appears, replace the Pixel Size value (1.0) with the number calculated above.
 * 14) Click OK.
 * 15) Click Tools -> Save configuration settings as... and overwrite the current configuration file.