Motor Controls (r3.8)

• Overview
• Section A: Current Motor Position
• Section B: Image Stack Acquisition
• Section C: Storing/Loading Motor Positions
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  • Resetting Motor Operation Following Faults

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Overview

The Motor Controls panel pertains to the (optional) control of a stage/motor controller system supported by ScanImage. See the ScanImage Hardware Reference for information about the currently supported controllers/stages.

The Motor Controls panel only appears on ScanImage startup if

is enabled in the INI File. Other settings related to the MP-285 must also be properly configured in the INI File, including the correct specification of the COM port used to communicate with the MP-285 over an RS-232 (serial port) connection.

If a Secondary Z motor controller is activated in the INI File (

specified), and the primary motor controller is configured as

='XYZ', then the Motor Controls controls 4 dimensions in total (the XYZ-Z configuration), as shown at right above. In all other configurations, (XY, Z, XYZ, XY-Z), 3 dimensions are shown, as at left above (inactive dimensions, if any, are shown with value 0).

Section A: Current Motor Position

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  : These controls play two roles –
  • They display the most recent position read from the motor controller in each of the 3-4 axes.
  • Entering a value for any of the axes commands the motor to move to the specified position for that axis. Following the move, the position will be read and updated for all three axes.

ScanImage always reads the Motor Absolute position from the motor. By default (at ScanImage startup), ScanImage displays and interprets positions in Motor Absolute coordinates. This remains true until (and only if) coordinates are converted to ScanImage Relative coordinates by pressing one of the

buttons.

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  : Forces ScanImage to read the current motor position in all three axes and to update the displayed
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  values, e.g. following manual adjustment of the motor position using the motor controller outside of ScanImage control.

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  : Read-only control that displays the squared-sum of the 3-4 displayed
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  values
  This is most useful when using ScanImage Relative coordinates in all 3-4 axes, as it then indicates the distance from the ScanImage Relative origin.

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  : Pressing these buttons forces ScanImage Relative positions to be used in the specified axes (if not used already) and resets the relative origin in the specified axes to the current position (which is first read from the motor controller).

Once ScanImage Relative positions are used in a particular axes, there is no returning to Motor Absolute coordinates. Pressing

again simply sets a new ScanImage Relative origin (in the specified axes).

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  : In 4-dimension XYZ-Z case, enabling/disabling this checkbox determines whether primary (disabled) or secondary (enabled) Z motor controller pertains for:
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    operation
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    step with arrow controls
  • Stack acquisitions

In 4-dimension XYZ-Z case, the

operation sets ScanImage relative origin for all 4 dimensions (i.e. regardless of the

checkbox state).

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  Arrows/Steps: Increment or decrement stage position in X, Y, or Z dimension by the specified step, in microns. In 4-dimension XYZ-Z case, the
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  value determines which motor controller is used when incrementing/decrementing the Z position.

Section B: Image Stack Acquisition

These controls allow the collection of Image Stack. When the value of

is greater than 1, an Image Stack is implied for each GRAB or LOOP Repeat. Each Slice is an individually triggered acquisition taken at a distinct axial (Z) position, consisting of one or more Frames as specified by

on the Main Controls panel.

The controls in this section also allow the endpoints of the Image Stack to be determined interactively, e.g. by manually focusing to axial (Z) boundaries of a volume-of-interest while using FOCUS mode acquisition.

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  Specifies the number of Slices to collect during the Image Stack acquisition

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  Specifies the axial (Z) step to take with the stage/motor controller between each Slice
  Either a positive or negative value can be specified, so the motion may proceed in either axial direction

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  : Specifies that stage/motor controller returns to the Home position – the initial position when GRAB or LOOP is initiated – following the GRAB acquisition or LOOP Repeat, so that subsequent acquisitions or Repeats occur at the same axial positions.
  If this option is not enabled when using LOOP mode, then successive Repeats will image progressively further along the axial direction specified
  If
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  is disabled, the first Slice in the Image Stack (or first Image Stack within a LOOP acquisition) is taken at the Home position – i.e. the motor does not move until after the first Slice is acquired.
  At this time, external triggering is not supported for Image Stack acquisitions

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  : If enabled, motor position at start of Image Stack acquisition is taken as the center of the stack. Motor is moved backwards by half the total span implied by
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  and
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  prior to the start of the stack acquisition.
  If
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  is even, then no Slice acquisition will occur at exactly the starting

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  : Button functions equivalently to
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  button one Main Controls panel except that, before the acquisition:
  • Motor is moved to Z position set as
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  • If
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    is enabled on the Power Controls, power is adjusted to value measured for each beam(s) when
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    was last set
    In addition, this
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    button must be used for
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    to have an effect (see below)

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  Pressing one of these buttons reads the current motor position in the Z axis (updating the
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  position display) and stores this value as the
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  position displayed alongside the buttons. In addition, the start and end powers are measured and stored, which can be recalled on Image Stack acquisitions started by
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  on Motor Controls, subject to other controls described below.
  The
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  value has no effect, unless
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  is selected
  The coordinates displayed are in either ScanImage Absolute or Relative coordinates, depending on whether
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  represents Absolute or Relative positions (i.e. whether
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  or
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  has been selected since ScanImage started).

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  If enabled, adjustments to either
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  or
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  will automatically adjust the other parameter, so that the
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  values defined remain in effect.
  If the checkbox is deselected, any change to the
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  or
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  will clear the stack start/endpoints.

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  :
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  When

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  is selected, stack acquisitions initiated via the

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  button on the Motor Controls panel (rather than from Main Controls) will override the

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  (power length constant) value on the Power Controls panel (assuming

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  is enabled on that panel). Instead the Lz value is computed from power levels measured at the endpoints of the stack determined by the

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  buttons.
  
  With

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  selected, user will typically use

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  mode to adjust power and Z position at both the start and end points of stack, pressing

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  and

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  buttons at each point, respectively to record both the Z position and power level(i.e. using a higher power at the deeper endpoint). Then Lz can simply be computed and this value is used instead of that specified in the Power Controls panel
  
  When

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  is used, the computed Lz value is displayed to Matlab command line, for each beam. Users may find that this is a useful way to measure/determine Lz for their preparation. User can then simply enter this value in the

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  control on the Power Controls panel and save value to USR file. Assuming that value is fairly consistent from sample to sample (for given sample type), this avoids need to adjust and record power at both start and end points of each stack.

  If multiple Beams are used, a separate Lz value is computed/used for each beam, i.e. power level for each Beam is measured independently at each endpoint.

Section C: Motor Positions

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  : Indicates the Position ID matching the last-read motor position (shown in
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  display), if any, to within the current Position Tolerance. User can select another Position ID from the dropdown menu to initiate motor move to those stored position coordinates.
  If current position does not match any currently defined Position ID, then an empty string is displayed.

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  : Read the current motor position (updating the
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  display) and create new identified Position in the Position Controls panel.

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  : Show/hide the Position Controls panel.