MOTOR CONTROLS Panel
3 dimensions (left); 4 dimensions (right)
- Overview
- Section A: Current Motor Position
- Section B: Image Stack Acquisition
- Section C: Storing/Loading Motor Positions
Unknown macro: {set-data}Unknown macro: {set-data}[Volume Imaging]
Overview
The MOTOR CONTROLS window pertains to (optional) control of a stage/motor controller system supported by ScanImage.
The Motor Controls panel only appears on ScanImage startup if a motorControllerType is specified in the
. Other motorXXX settings in the
pertain to this controller, if specified - e.g. the COM port controller is connected to if it is serial-port controlled.
If a Secondary Z motor controller is activated in the
(by specifying the motor2ControllerType), and the primary motor controller is configured with motorDimensions='XYZ' (the default value), then MOTOR CONTROLS controls 4 dimensions in total (termed 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
ScanImage vs Motor Relative
ScanImage has its own notion of relative positions, independent of the relative coordinates maintained by some motor controllers, such as the Sutter MP285
. To make this distinction clear, the coordinate sets are referred to below as ScanImage Relative and Motor Relative.
- Unknown macro: {blue}: 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.
- Unknown macro: {blue}: Forces ScanImage to read the current motor position in all three axes and to update the displayedUnknown macro: {blue}values, e.g. following manual adjustment of the motor position using the motor controller outside of ScanImage control.
- Unknown macro: {blue}: Read-only control that displays the squared-sum of the 3-4 displayedUnknown macro: {blue}values
- Unknown macro: {blue}: 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).
- Unknown macro: {blue}: In 4-dimension XYZ-Z case, enabling/disabling this checkbox determines whether primary (disabled) or secondary (enabled) Z motor controller pertains for:
- Unknown macro: {blue}operation
- Unknown macro: {blue}step with arrow controls
- Image Stack acquisitions (for standard, stepping stacks)
Matching Relative Coordinates
A common and recommended approach is to set both the motor controller and ScanImage to operate in matched Relative coordinates. The procedure to accomplish this is as follows:
1. Adjust the motor controller to display Motor Relative positions, if not already. (For the MP-285, display of Motor Absolute and Motor Relative positions is toggled by hitting <ENTR>)
2. Set the Motor Relative position to zero at some desired position. (For the MP-285, this is done by hitting <0>,<ENTR>).
3. Immediately afterwards, press
to set the ScanImage Relative position.
At this point, both the motor controller and ScanImage are operating in Relative coordinates, at position (0,0,0). If desired, these steps can be repeated later at new physical position(s), updating both Relative origins in tandem.
- Unknown macro: {blue}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, theUnknown macro: {blue}value determines which motor controller is used when incrementing/decrementing the Z position.
Section B: Image Stack Acquisition
These controls configure Image Stack acquisitions, of which ScanImage supports two types:
- Standard ('Slow Z') stepping stacks
- Volume Imaging ('Fast Z') stacks (when
Unknown macro: {blue}is selected in the FAST Z CONTROLS)
When value of
is greater than 1, an image stack acquisition is implied for each GRAB or LOOP Repeat. For standard stacks, 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 window. See
for more information about FastZ stacks.
Core Image Stack Controls
- Unknown macro: {blue}
- For standard stacks, specifies number of Slices to collect during an Image Stack acquisition.
- For
Unknown macro: {get-data}, specifies the number of frames acquired during each volume period.
- Unknown macro: {blue}
- For standard stacks, specifies axial (Z) step to take with the motor controller between each Slice.
- For
Unknown macro: {get-data}, specifies the axial distance traversed (e.g. swept) between successive frames in each volume period.
Either a positive or negative value can be specified, so motion may proceed in either axial direction
- Unknown macro: {blue}: If enabled, motor controller returns to Home position – the initial axial position when a GRAB or LOOP was initiated – following the GRAB acquisition or each LOOP Repeat. This ensures subsequent acquisitions or Repeats traverse the same axial positions.
For LOOP acquisitions, this option should typically be enabled. If not enabled, successive Repeats will image progressively further along the axial direction specified, which is typically not desired.
- Unknown macro: {blue}: If enabled, axial 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 byUnknown macro: {blue}andUnknown macro: {blue}prior to the start of the stack acquisition.
If
is enabled and
is even, then no Slice will be obtained or centered on the starting axial position at time of GRAB/LOOP initiation
Image Stack Endpoint & Power Controls
Often, users may wish to select the starting and ending axial positions, as well as the imaging power, interactively, i.e. during FOCUS when the axial position and power can each be adjusted during live imaging.
Endpoints for Slow Z Only
As of ScanImage 4.1, the stack position and power start/endpoint constraints only apply to standard (Slow Z) stacks. However, using interactive stack start & endpoint selection can still be useful for
to determine/set the
(length constant) value in POWER CONTROLS by using
.
- Unknown macro: {blue}: The starting axial position of stack can beUnknown macro: {blue}interactively. Motor controller will be moved to specified axial position at start of subsequent (standard) Image Stack acquisitions.
- Unknown macro: {blue}: The ending axial position of stack can beUnknown macro: {blue}interactively. When bothUnknown macro: {blue}andUnknown macro: {blue}are set, the values ofUnknown macro: {blue}andUnknown macro: {blue}are constrained so that Image Stacks traverse the specified axial extent.
The constraint on
and
remains in effect until either
or
is pressed.
If
is enabled for a particular
on the POWER CONTROLS window, the following controls pertain:
: Power to use at starting axial position of stack can be
interactively. If
is enabled, then power is adjusted to this level (for selected/displayed
) at start of subsequent (standard) Image Stack acquisitions.
: Power to use at ending axial position of stack can be
interactively. When both
and
are set, user can choose to automatically or manually
, i.e. override the length constant
set on the POWER CONTROLS for the selected
, with the exponential length-constant value implied by (computed from) the start/end positions and powers.
: When
and
values are all
, the
(length constant) value in POWER CONTROLS can be overridden with value computed from the specified position/power endpoints.
- With checkbox enabled, the POWER CONTROLS
Unknown macro: {blue}value is automatically overridden when all endpoints are set
- With checkbox disabled, button can be used to manually override POWER CONTROLS
Unknown macro: {blue}value
When
or
are
, current power values are captured/stored for each Beam. Stored value for only the currently selected
in POWER CONTROLS is shown at a time.
values are stored for Beams for which
is disabled on POWER CONTROLS have no effect
Set Lz Once
The
length constant values for each Beam are saved as part of the ScanImage User Settings (*.USR) file. For a given specimen type, the length constant describing the additional power required as a function of depth can be expected to remain generally constant. Thus, users may typically set the power and position levels interactively (spanning a wide axial extent) and manually select
to compute the length constant. Then this value can be saved to the *.USR file, avoiding requirement to interactively set/determine the length constant in future ScanImage sessions.
Section C: Motor Positions
ScanImage can store sets of motor controller coordinates ('positions') which can be later revisited and/or stored into position (.POS) files.
- Unknown macro: {blue}: Reads motor controller coordinates (including Secondary Z coordinate if XYZ-Z configuration is used) updatingUnknown macro: {blue}values. Creates new Position ID at these coordinates, shown in the POSITION CONTROLS window.
- Unknown macro: {blue}: Show/hide the POSITION CONTROLS window, which allows user to revisit previously stored motor positions.