\ACTIVATELASER\ N

Activate laser number N, where N is a zero-based number (first laser
is 0). This is only applicable to Laser Module-equipped microscope
systems.

\ACTIVE\ [ON | OFF]

Switch on or off a variety of display functions, including histogram
display and autoranging, and intensity autoscaling. This is typically
only used internally, not in an experiment Macro.

\ACTSHUT\ N

Enables or disables illumination and camera shutters. N is an 8-bit
number  (between 0-255) that describes  which shutters to activate.  
Bits 1-4 correspond to illumination  shutters and bits 1-4 correspond
to  camera shutters.  For example, N=17  indicates that illumination
shutter 1  and camera shutter 1 should be active.

\AUTOFOCUS\ [EX_FILTER,Z_TEST_STEP,MAX_Z_RANGE,
             CONTRAST_CALC,POST_Z_OFFSET]

Autofocus the optics based on image contrast using the current XY
position and camera settings. The depth-of-field, maximum Z range,
contrast  calculation method, and Z offset will be  automatically
determined if not provided.

Optional Arguments:
  EX_FILTER      The index of the EX filter to use (0-based)
  Z_TEST_STEP    The step size of the search. This
                 is usually the objective depth-of-field (um).
  MAX_Z_RANGE    Z range to search (um, top to bottom).
  CONTRAST_CALC  Contrast calculation method.
                 0 = autodetermine
                 1 = light on dark (epi/fluorescence)
                 2 = dark on light (trans/brightfield)
  POST_Z_OFFSET  The Z distance (um) to move after 
                 finding the maximum contrast.

\AUTOFOCUS_EXP\ [EX_FILTER,EXP,Z_TEST_STEP,MAX_Z_RANGE,
             CONTRAST_CALC,POST_Z_OFFSET]

Autofocus the optics based on image contrast using the current XY
position and camera settings. The depth-of-field, maximum Z range,
contrast  calculation method, and Z offset will be  automatically
determined if not provided. Same behavior as the AUTOFOCUS command
except that an explicit base exposure time is added. 

Optional Arguments:
  EX_FILTER      The index of the EX filter to use (0-based)
  EXP            The base exposure time for the Autofocus Algorithm
  Z_TEST_STEP    The step size of the search. This
                 is usually the objective depth-of-field (um).
  MAX_Z_RANGE    Z range to search (um, top to bottom).
  CONTRAST_CALC  Contrast calculation method.
                 0 = autodetermine
                 1 = light on dark (epi/fluorescence)
                 2 = dark on light (trans/brightfield)
  POST_Z_OFFSET  The Z distance (um) to move after 
                 finding the maximum contrast.

\AUTORANGE\ [ON | OFF]

Switch on or off the histogram autoranging.

\AUTOSCALE\ [ON | OFF]

Switch on or off the image intensity
autoscaling.

\AVG\ [NPIC,SECONDS,NODIVIDE]

Average npic images, each with exposure time of seconds.  In
situations where it is undesirable to divide the image intensity by
npic, set the nodivide flag to 1.

Default: 
     npic=8
     seconds=current exposure time in Resolve3D
     nodivide=0.
See also CCD and EXP.

\BEEP\

Sound the keyboard bell.  A good time to use BEEP is before camera
exposures in a time-lapse experiment.

\BIN\ N

Add NxN detector elements together during camera readout.  This will
shorten the readout time, but lower the resolution. Binning will also
reduce the necessary exposure time in proportion to the number of
binned elements.  Default: N=1.

\BLANKSCREEN\
Blank the workstation and controller display screens.

\CAMTEST\ [FILENAME]

Perform a series of camera tests.  Test results are placed in a file
called "filename", within the data directory 

\CCD\ [SECONDS]

Acquire a CCD image with exposure duration seconds.  The minimum
exposure is 0.001 seconds (1 msec).  Default: seconds=current
exposure time in Resolve3D.  See also AVG, EXP, and, DARK.

\CCDSETUP\

Sets up the CCD camera hardware according to the current conditions
specified by Resolve3D.

\CLF\

Close the active file.  See also OPF, WRT, and WRTF.

\CLF2\

Close all files opened by OPF2. See also FIRSTPOINT, NEXTPOINT,
POINTLIST, OPF2, WRT2, and WRT2F.

\CLF_DSSI\ FILE_TAG1,FILE_TAG2...FILE_TAGn

Close open Localization image files specified by the FILE_TAG[n] arguments.

\CLF_REF\

Close an open Reference Image file.

\CLF_SETHEADER\ nZ,nW,nT

Close the active file and force the header arrangement to be the
specified nZ, nW, nT. This command is available for custom experiment
macros whose Z, W, and T arrangment  can not be determined by the
software. Use this command with caution. 

\CLF2_SETHEADER\ nZ,nW,nT

Close all open Point Visit files and force the header  arrangement to
be the specified nZ, nW, nT. This command  is available for custom
experiment macros whose Z, W, and  T arrangment can not be determined
by the software. Use  this command with caution. 

\CMASS\ [FRACTION]

Calculate the center of mass of the  most recently acquired image.
Subtract the minimum image intensity unless a fractional value is
provided. FRACTION determines the amount of background  subtraction.
FRACTION=0.5 will subtract an amount 1/2 way between the min and max
image intensity. Use FRACTION=0 to bypass subtraction.

\DARK\ [SECONDS]

Acquire a dark current image. The minimum exposure is 0.001 seconds
(1 msec). Default: seconds=current exposure time in Resolve3D.  See
also AVG, CCD, and, EXP.

\DISBANK\ [N]

See the USEBANK command.

\DISDATA\ [N]

Display an image previously displayed in the current window and
bank.  N represents the number of images to retrace, relative to the
image currently displayed.  Default: display the most recent image.

\DISPLAY\ [ON | OFF]

Switches on or off the display of images. This is useful when faster
data collection is desired.  See also STATS and ACTIVE.

\DISWIN\ [N]

See the USEWIN command.

\DO\ LOOPS

Loop through the subsequent commands, up to the ENDDO command, loops
times.  See also ENDDO. Replaces obsolete command NDO.

\DOLASEREVENT\ DURATION

Opens the laser shutter for specified DURATION (in seconds).

Available on QLM and X4 equipped systems only.

\DO_CELL_TRACK\

Track cell movements and make stage adjustments to keep cells of
interest in the field-of-view.

\DSSI_MASR\ CAM_NUM,DEP_LASER,DEP_PWR,DEP_DUR,PRE_ACT_NIMGS,
            IMG_LASER_PWR,UFFREQ,UFDOF,UFTHR,UFITER,
            IMG_EX,IMG_EM,IMG_ND,IMG_EXP,
            IMG_SHT,IMG_EX_SHT_MODE,
            PS_RPTS,PS_NACT,
            [PS_ACT_CHAN_1,PS_ACT_PWR_1,PS_ACT_DUR_1,PS_ACT_NIMG_1 ...
             PS_ACT_CHAN_n,PS_ACT_PWR_n,PS_ACT_DUR_n,PS_ACT_NIMG_n]
        
Localization (Multi-Activation, Single Reporter) Scan

Parameters:
 CAM_NUM:       Camera number
 DEP_LASER:     Depletion laser number (unused, same as IMG_EX)
 DEP_PWR:       Depletion laser power 
 DEP_DUR:       Depletion phase duration (0.0 turns pre-activaion
                 depletion Off)
 PRE_ACT_NIMGS: Number of images to take before first activation
 IMG_LASER_PWR: Power for imaging laser
 UFFREQ:        UltimateFocus frequency (in terms of pulse sequence)
 UFDOF:         UltimateFocus depth-of-field
 UFTHR:         UltimateFocus move threshold (nanometers)
 UFITER:        UltimateFocus maximum iterations to try for correction
 IMG_EX:        Imaging EX channel index 
 IMG_EM:        Imaging EM channel index
 IMG_ND:        Imaging Neutral Density
 IMG_EXP:       Exposure time 
 IMG_SHT:       Imaging Shutter Mask (unused)
 EX_SHT_MODE:   Imaging Shutter Behavior:
                    1: continuous
                    2: pulsed
 PS_RPTS:       Pulse Sequence Repeats
 PS_NACT:       Pulse Sequence Number of Activations
  [for each activation defined...]
    PS_ACT_CHAN: Pulse Sequence Activation Channel index
    PS_ACT_PWR:  Activation pulse duration
    PS_ACT_DUR:  Pulse duration
    PS_ACT_NUMG: Number of images following each Activation Pulse

\EMFILTER\ EMFILTERNAME

Move the emission filter wheel to emfiltername.  See also EXFILTER
and NDFILTER.

\ENDDO\

Last line of the loop created by DO. Also see DO.

\ENDIF\

Marks the end of processing of a conditional block of the experiment
macro. See documentation for the IF macro command.

\EXFILTER\ EXFILTERNAME

Move the excitation filter wheel to exfiltername. See also EMFILTER
and NDFILTER.

\EXP\ SECONDS

Set Resolve3D's default exposure time in seconds for CCD image
acquisition. The minimum exposure is 0.001 seconds (1 msec). See also
AVG, CCD, and DARK.

\FILTERS\ EXFILTERNAME,EMFILTERNAME,NDFILTERNAME

Move all the filter wheels as efficiently as possible to the
specified positions. See also EMFILTER, EXFILTER, NDFILTER commands.


\FINDEXP\

Find the exposure time required to reach the current target
intensity.

\FINISH_CELL_TRACK\

Used at the end of a cell-track experiment to reset system states. 

\FIRSTPANEL\ [ ULTFOCUS Maintain,UF_THR,UF_ITER ] or
             [ AUTOFOCUS [AF_ARGS] ]

Move to the location of the first panel defined by the PANEL
command.  See also PANEL and NEXTPANEL.

Optional parameters:

 ULTFOCUS Maintain,UF_THR,UF_ITER: Do UltimateFocus maintenance using
   UF_THR as the move threshold and UF_ITER as maximum iterations
   
 AUTOFOCUS: Do a contrast-based Autofocus. See AUTOFOCUS for a 
   description of optional AF_ARGS

\FIRSTPOINT\

Move to the first point in the point list. See also NEXTPOINT,
POINTLIST, OPF2,  WRT2, WRT2F, and CLF2.

\FIRST_T\

Used internally as a "marker" to specify the first time point. This
is used in "IF" conditional processing.

\FIRST_W\

Used internally as a "marker" to specify the first wavelength. This
is used in "IF" conditional processing.

\FIRST_Z\

Used internally as a "marker" to specify the first Z section. This
is used in "IF" conditional processing.

\FLIP\ N

Specify the CCD chip orientation.  The default orientation is
specified in Resolve3D.SYS.

\FOCUS\ dZ

Move the objective lens' focal plane by dZ microns.

\GAIN\ X

Set the camera gain to value X.  Valid values of X depend on the
camera type.  Typical gain values are 1X and 4X.

\GETXYZ\

Get the XYZ position of the microscope stage and report it to the
status window.

\GETZ\

Get the Z position of the microscope stage or objective lens and
report it to the status window.

\HIST\ [ON | OFF]

Turn the Resolve3D histogram display on or off.

\IC\ "COMMAND"

Send "command" directly to the instrument  control computer.  For a
description of valid commands, refer to DeltaVision technical
documentation. Formerly known as "PCTALK".

\IF\ [T=i,j... | Z=i,j... | P=i,j...]

Conditionally process the macro commands between this and the next
ENDIF. T and Z and P (point number) are recognized. For example, to
execute a pause during the first and third time point, the
conditional would look like:

DO 10
    IF T=1,3
       PAUSE
    ENDIF
    ...
    TLAPSE 10
ENDDO

See the Information Button [?] in the Actions tab of Design/ Run
Experiment to see a full description of the conditional 
specification syntax.


\INIT_CELL_TRACK\ REF_CHAN,CENTER_METHOD,ROI_PERCENT,THRESHOLD

Initialize Cell Track parameters:
REF_CHAN:      Reference channel number
CENTER_METHOD: "Center of Shape" or "Center of Intensity"
ROI_PERCENT:   Percent of total ROI to consider
THRESHOLD:     Change threshold (microns) to trigger a
               stage movement.

\LAMPS_OFF\

Turn off all arc lamps that are under the microscope's control. This
is intended to be used at the end of an experiment macro and should
be used cautiously. Cycling lamps On and Off too frequently will
shorten bulb life. 

\LASER_ON_OFF\ LASER_INDEX [ON | OFF]

Turn the specified laser (0-based laser index) On or Off. With no
argument, it will set the laser On.

\LASERSHUT\ [SECONDS]

Open the laser shutter for the specified time. (Same as DOLASEREVENT)

\LENS\ LENSNAME

Set the lens to lensname.  A list of valid lens names can be found in
the Resolve3D.SYS configuration file and also the pull-down list in
Resolve3Ds program window.

\LMCMOVE\ [True | False]

Perform an LMC (Lost Motion Compensation) move of the microscope
stage. An argument of True triggers LMC in X,Y, and Z; an argument
of False triggers Z LMC only.

\LOCAL\

Set the DeltaVision Controller to "local" mode. See also REMOTE.

\LOGNOTE\ "NOTE TEXT"

Adds a comment and time-stamp to the current  data collection log
file.

\LOGNOTE_CUR_PT\ "NOTE TEXT"

Adds a comment and time-stamp to (only)  the currently-visited
point's data collection log file.

\MAG\ [ON | OFF]

Inform Resolve3D that the auxiliary magnifier  is in, or out, of
place.  Many manufacturers refer to the auxiliary magnifier as an
optivar.  

\MASTAGE\ X,Y,Z

Move the XYZ stage to coordinate (x,y,z) in
microns.

\MATRIX_SCAN\ NROWS,NCOLS,H_SPACING,V_SPACING,SCANPAT,
     AF_METHOD,AF_MODE,AF_CHANNEL,AF_EXP,AF_BIN,AF_LONG,
     AF_SHORT,NUMZ,ZSTEP,OAI_DEPTH,NUMW,
     EX1,EM1,ND1,EXP1,SHUT1... EXN,EMN,NDN,EXPN,SHUTN

Acquire a grid of panels relative to the currently-visited point.
Primarily used to sample areas within a well of a microtiter plate.

Arguments:
 NROWS      Number of rows of panels
 NCOLS      Number of columns of panels
 H_SPACING  Horizontal spacing between panels
 V_SPACING  Vertical spacing between panels
 SCANPAT    Pattern of panels within the scan
                0 = RASTER
                1 = SERPENTINE
 AF_METHOD  Autofocus method:
                0 = none
                1 = UltimateFocus hardware
                2 = Image-contrast based
                3 = both                  
 AF_MODE    Autofocus mode:
                0 = none
                1 = before first panel
                2 = all panels
 AF_CHANNEL Channel number for image-contrast autofocus
 AF_EXP     Exposure for autofocus
 AF_BIN     Binning for autofocus
 AF_LONG    "long" Z search range for well-to-well 
                       image-contrast autofocus
 AF_SHORT   "short" Z search range for panel-to-panel 
                       (within well) image-contrast autofocus
 NUMZ       Number of Z sections.
 ZSTEP      Z Step Size for non-OAI sectioning
 OAI_DEPTH  Negative number means no OAI
 NUMW       Number of wavelengths.
 EX1        Excitation filter position number 1.
 EM1        Emission   filter position number 1.
 ND1        ND         filter position number 1.
 EXP1       Exposure time number 1, in seconds.
 SHUT1      Shutter mask 1.  8 bit mask. (see ACTSHUT)
 ...
 EXN        Excitation filter position number n.
 EMN        Emission   filter position number n.
 NDN        ND         filter position number n.
 EXPN       Exposure time number N, in seconds.
 SHUTN      Shutter mask N.  8 bit mask. (see ACTSHUT)


\MESSAGE\ "MESSAGE TEXT"

Send "message text" to the status window.

\MIRROR\ POSITION

For systems equipped with an Olympus motorized dichroic mirror, this
command can be used to move the mirror to a specified position. The
POSITION argument is an integer in the range 1 to 6.

\MRSTAGE\ dX,dY,dZ

Move the XYZ stage by (dX,dY,dZ) microns, relative to the current
location.  See also MASTAGE.

\MULTIPLY\ BKG1,BKG2,SCALE,[MARK_POINT, THRESHOLD]

Multiply the two most recently collected images
and generate a product image. 
BKG1:       Background to subract from image 1
BKG2:       Background to subtract from image 2
SCALE:      Scale the product image by this amount

Optional Arguments:
MARK_POINT: Mark the current stage point
THRESHOLD:  Only mark the point if the mean is
            greater than this value.

\MZSTAGE\ dZ

Move the Z stage by dZ microns.  This command works only with systems
having a Z stage (as opposed to motorized focus). See also FOCUS.

\NDFILTER\ NDFILTERNAME

Set the neutral-density filter to ndfiltername.  A list of the valid
filter names can be found the pull-down list in Resolve3D's program
window. See also EXFILTER, EMFILTER and FILTERS.

\NEXTFILE\

Increment the current file number. Note that the NEXTFILE step occurs
automatically whenever NEXTPOINT is used.  See also NEXTPOINT.

\NEXTPANEL\ [ ULTFOCUS Maintain,UF_THR,UF_ITER ] or
              [ AUTOFOCUS [AF_ARGS] ]

Move to the location of the next panel.  See also PANEL and
FIRSTPANEL.

Optional parameters:

 ULTFOCUS Maintain,UF_THR,UF_ITER: Do UltimateFocus maintenance using
   UF_THR as the move threshold and UF_ITER as maximum iterations
   
 AUTOFOCUS: Do a contrast-based Autofocus. See AUTOFOCUS for a 
   description of optional AF_ARGS

\NEXTPOINT\

Move to the next point in the list and activate the corresponding
image file. See also FIRSTPOINT, POINTLIST, OPF2,  WRT2, WRT2F, and
CLF2.

\NEXT_T\

Increments an internal counter for "IF" conditional processing.

\NEXT_Z\

Increments an internal counter for "IF" conditional processing.

\NOISECALC\

Calculate the camera noise in counts.

\OPF\ [FILENAME]

Open an image file with the name filename. The image file will be
stored in the default data directory.  Omission of  filename causes a
user prompt.   See also WRT, WRTF, and CLF.

\OPF2\ POINT_LIST

Open image files for the listed points. The image files will be
stored in the default data directory. See also FIRSTPOINT, NEXTPOINT,
WRT2, WRT2F, and CLF2.

\OPF_DSSI\ FILE_TAG1,FILE_TAG2...FILE_TAGn

Open image files for Localization image acquisition with the names
 specified by FILE_TAG[n]

\OPF_REF\

Open a reference image file.

\PAIR\ EMFILTERNAME EXFILTERNAME

Pair the excitation filter exfiltername with the emission filter
emfiltername.  A list of the valid filter names can be found in the
pull-down list in Resolve3Ds program window.  The PAIR command
overrides the default pairings.  See also EMFILTER and EXFILTER.

\PANEL\ START_X,START_Y,END_X,END_Y,OVERLAP_X,OVERLAP_Y,NUMBER_PANELS

Setup panel collection sequence.  The start and end coordinates
correspond to opposite corners of the area to be scanned.  A
serpentine scan pattern will be used to acquire images over the
entire area. All positions  are in microns. Panel overlapping is used
to make sure  that no area is missed.  A distance corresponding to 
two pixels is recommended.  The number of panels required  to scan
the area should equal NUMBER_PANELS, otherwise an error will be
generated and the macro will not run. This situation can occur if the
magnification (that is, pixel size) has been changed.

\PD\ "COMMAND"

Send  "command" command to the photodiode. For a description of valid
commands, refer to DeltaVision technical documentation.  See also PC.

\POINTLIST\ POINT_LIST

Setup the listed points for multi-point visiting. Point list format
example: 1-3,5,7-9 See also FIRSTPOINT, NEXTPOINT, OPF2, WRT2, WRT2F,
and CLF2.

\QLM_EVENT\ LASERNO,DURATION,EVENTPATTERN,EVENTPOINTSET,EVENTREPEATS,
            BACKLASH,PRE_Z_MOVE,POST_Z_MOVE

Execute the specified Laser event using the QLM or X4. This macro is
intended to be used internally by the Actions mechanism.

LASERNO:       Laser Number (1-based)
DURATION:      Laser Pulse Duration in seconds.
EVENTPATTERN:  0 indicates Center point, 1 indicates a 
                 pattern bleach
EVENTPOINTSET: Number of the bleach event point set (1-based).
                 This corresponds to the lettered sets ("A,B,C...")
                 In the Laser Action Options user dialog box. 
EVENTREPEATS:  Number of times to execute event
BACKLASH:      Backlash Z move distance
PRE_Z_MOVE:    Distance to move from "current" Z
                 coordinate before event
POST_Z_MOVE:   Distance in Z to move after event 

\RATIO\ [BACKGROUND1,BACKGROUND2]

Calculate the ratio image of the most  recently acquired image
(denominator) and the second most recent image (numerator).
BACKGROUND1 and BACKGROUND2 are subtracted from the numerator and
denominator, respectively, before  calculating the ratio.  As with an
image from the CCD command, use the WRT, WRTF, WRT2, or WRT2F 
command to save the image to an open file.

\RECORD\

Record the current XYZ location as a point to visit. See also VISIT.

\REF_IMG\ REF_IMG EXP,EX,EM,ND,SHUTTERMASK,
                BACKLASH,PRE_Z_MOVE,POST_Z_MOVE

Acquire a Reference Image and write it to an open reference image
file.

Arguments:

EXP:         Exposure time in seconds
EX:          Excitation filter name
EM:          Emission filter name
ND:          Neutral density (% Transmission) filter name
SHUTTERMASK: Bitmask of shutters to enable (see ACTSHUT)
BACKLASH:    Z backlash move in microns
PRE_Z_MOVE:  Z distance to travel before imaging
POST_Z_MOVE: Z distance to travel after imaging

\REMOTE\

Set the DeltaVision Controller to "remote" mode.  See also LOCAL.

\REPLACEPOINT\ PT_NUMBER[,True | False]

Replace the specified marked point number with the current stage
position. If the optional argument is True, the user will be asked to
confirm this action.

\RESETPC\

Reset the Instrument Control PC.

\ROTSPEED\ N

Set the filter wheel rotation speed. Valid values for N are between 1
and 100.  The default is 1.

\SAVEDEF\

Save the current system configuration in a file called Resolve3D.def
for later use.

\SCANOAI\ SAVE_MODE,NUMZ,ZSTEP,ZTYPE,ZBACKLASH,NUMW,
                EX1,EM1,ND1,EXP1,CAM1,CAMMODE1,SHUT1, ...
                EXN,EMN,NDN,EXPN,CAMN,CAMMODEN,SHUTN
                [,NUMT,TLAPSE]
          
  SAVE_MODE  Save images if a file is open.
               0 = don't save
               1 = save in a single file (WRT)
               2 = save in the next file of the point list (WRT2)
  NUMZ       Number of Z steps.
  ZSTEP      Z step size, in um.  Use negative values for standard 
               scan direction. Positive for reverse.
  ZTYPE      Z scan type:
               0 = start at current location
               1 = start at center
               2 = start at end
  ZBACKLASH  Z backlash removal size. (<= 0 means no backlash removal.)
  NUMW       Number of wavelengths.
  EX1        Excitation filter position number 1.
  EM1        Emission   filter position number 1.
  ND1        ND         filter position number 1.
  EXP1       Exposure time number 1, in seconds.
  CAM1       Camera number 1.  Normally CAM1=1.
  CAMMODE1   Camera 1 readout mode.
               0 = normal
               1 = slow
               2 = medium
               3 = fast
               4 = very fast
  SHUT1      Shutter mask 1.  8 bit mask.
  ...
  EXN        Excitation filter position number n.
  EMN        Emission   filter position number n.
  NDN        ND         filter position number n.
  EXPN       Exposure time number N, in seconds.
  CAMN       Camera number N.  Normally CAMN=1.
  CAMMODEN   Camera N readout mode.
               0 = normal
               1 = slow
               2 = medium
               3 = fast
               4 = very fast
  SHUTN      Shutter mask N.  8 bit mask.

  NUMT       Number of time points. An optional parameter. 
               Default NUMT=1.
  TLAPSE     Time lapse in seconds. An optional parameter. 
               Default TLAPSE=0.      

      
\SCANPK\ EXPOSURE_SECS,SHUT_PATTERN,TIMING_METHOD,CAM_MODE,
         EX_NUM,EM_NUM,ND_NUM,IMAGE_BETWEEN,LASER_NUM,
         LASER_POWER,PULSE_DURATION,EVENT_PATTERN,
         T0_MARK,EVENT_REPEATS,NUM_PRE_IMAGES,NUM_POST_IMAGES,
         EXPECTED_HALFTIME,TOTAL_TIME,NUM_SEGMENTS,TIMING_STYLE,
         PRE_IMAGE_INTERVAL

Start a PK experiment.

Arguments:
  EXPOSURE_SECS      Image exposure time in seconds,
  SHUT_PATTERN       Shutter pattern mask for imaging.  8 bit pattern.  
                     See the ACTSHUT command.
  TIMING_METHOD      Image acquisition timing method. 
                       0 = adaptive
                       3 = as fast a possible.
  CAM_MODE           Camera 1 readout mode:
                       0 = normal
                       1 = slow
                       2 = medium
                       3 = fast
                       4 = very fast
  EX_NUM             EX filter position number (0 based)
  EM_NUM             EM filter position number (0 based)
  ND_NUM             ND filter position number (0 based)
  IMAGE_BETWEEN      Acquire images between repeated laser events.  
                       Usually 0. (0=no, 1=yes)
  LASER_NUM          Laser number to use (1 based)
  LASER_POWER        Laser power in percent.
  PULSE_DURATION     Laser pulse duration in seconds.
  PATTERN_NUM        Event pattern number to use (0=don't use a 
                       pattern, don't move the XY location)
  T0_MARK            T0 marking method 
                       0 = don't change T0 mark
                       1 = use the start of the laser event as T0
                       2 = use the middle of the laser event as T0
                       3 = use the end of the laser event as T0
  EVENT_REPEATS      Number of times to repeat the event (usually 1)
  NUM_PRE_IMAGES     Number of images to acquire before the event.
  NUM_POST_IMAGES    Number of images to acquire after the event.
  EXPECTED_HALFTIME  The expected half-time of the recovery (or 
                       dispersion).
  TOTAL_TIME         The total time of imaging after the laser event.
  NUM_SEGMENTS       Number of different timing segments within the 
                       image acquisition phase.
  TIMING_STYLE       Method of timing image acquisitions 
                       0 = uniform timing 
                       1 = adaptive
  PRE_IMAGE_INTERVAL Seconds between images during the pre-event 
                       phase.

\SCANZWT\ SAVE,SHTYPE,SEQUENCE,NUMZ,ZSTEP,ZTYPE,ZBACKLASH,
               NUMW,EX1,EM1,ND1,EXP1,CAM1,CAMMODE1,SHUT1,...
               EXN,EMN,NDN,EXPN,CAMN,CAMMODEN,SHUTN
               [,NUMT,TLAPSE]

Request a Z, wavelength, and time scan from the instrument
controller.  Valid for network  camera systems only.

Arguments:
  SAVE       Save images if a file is open.
                0 = don't save
                1 = save in a single file (WRT)
                2 = save in the next file of the point list (WRT2)
  SHTYPE     Shutter control type:
                0 = no changes
                1 = open & close for every exposure.
                2 = open & close once for every Z scan.
                3 = open & close once for every ZWT scan.
  SEQUENCE   Scan sequence:
                1 = Wavelength then Z
                2 = Z then wavelength
  NUMZ       Number of Z sections.
  ZSTEP      Z step size, in um.  Use negative values 
             for standard scan direction. 
             Positive for reverse.
  ZTYPE      Z scan type:
                0 = start at current location
                1 = start at center
                2 = start at end
  ZBACKLASH  Z backlash removal size. 
             (<=0 means no backlash)
  NUMW       Number of wavelengths.
  EX1        Excitation filter position number 1.
  EM1        Emission   filter position number 1.
  ND1        ND         filter position number 1.
  EXP1       Exposure time number 1, in seconds.
  CAM1       Camera number 1.  Normally CAM1=1.
  CAMMODE1   Camera 1 readout mode:
                0 = normal
                1 = slow
                2 = medium
                3 = fast
                4 = very fast
  SHUT1      Shutter mask 1.  8 bit mask.  
             See the ACTSHUT command.
  ...
  EXN        Excitation filter position number n.
  EMN        Emission   filter position number n.
  NDN        ND         filter position number n.
  EXPN       Exposure time number N, in seconds.
  CAMN       Camera number N.  Normally CAMN=1.
  CAMMODEN   Camera N readout mode:
                0 = normal
                1 = slow
                2 = medium
                3 = fast
                4 = very fast
  SHUTN      Shutter mask N.  8 bit mask.  
             See the ACTSHUT command.
 
  NUMT       Number of time points. 
             An optional parameter. Default NUMT=1.
  TLAPSE     Time lapse in seconds. 
             An optional parameter. Default TLAPSE=0.      


\SCANZWT_SETUP_RATIO\ TIMESPEC

This is an internally-generated macro command to tell the system how
to do ratio imaging with a Fast Acquisition time lapse. 

  TIMESPEC   Specification of a set of time
             points to use. 
             
             Valid Examples:
                 1-2
                 1,4,5
                 1-4,6-9
                 all

\SECTIONZ\ DZ

Specialized version of the "FOCUS" macro command that is for use in Z
sectioning loops. Recalculates absolute Z position with each call
instead of incrementing Z in a relative way. 

\SETLASERPOWER\ LASER_NUMBER,POWER

Set the power of the specified laser (a 0-based laser number) to the 
POWER value (percent).


\SETLMC\ AXISMASK

Switch on or off lost motion compensation (LMC) to reduce back-lash
errors. AXISMASK is a code described in this table:

   0 = no LMC on any Axis
   1 = X only
   2 = Y only
   3 = X + Y 
   4 = Z only
   5 = X + Z
   6 = Y + Z 
   7 = X + Y + Z

\SETUP_RATIO\ FIRST_CHANNEL_NUM, NUM_BKG, DENOM_BKG

Internally-generated command that sets up the  monitoring of a Ratio
Imaging experiment.  FIRST_CHANNEL_NUM can have the value of 1 or 0 
(representing True and False) to indicate if  the first channel is
the ratio's numerator. NUM_BKG is a value indicating the background 
to subtract from the numerator channel and  DENOM_BKG is the
denominator background in counts.

\SET_POLYCHROIC\ POLYCHROIC_NAME

Set the motorized Polychroic turret to put the named Polychroic
mirror in place. Only available on systems with a motorized
Polychroic turret.

\SET_TIRF_DEPTH\ LASER_INDEX, DEPTH_VALUE

Set the evanescent wave depth for the specified laser index (0-based)
to DEPTH_VALUE.

\SHIFTPOINTLIST\ DELTA_X DELTA_Y

Shift the entire in-memory point list by Delta_X and Delta_Y
(in microns). This will result in all points being marked as 
uncalibrated to the UltimateFocus system (if installed).

\SHOW_RATIO\ 

This command (in an experiment where SETUP_RATIO is called)
calculates and displays a ratio image  of the two most recent image
frames and plots  the mean of any specified ROIs (Regions Of 
Interest) on a graph to monitor a Ratio Imaging experiment.

\SIZE\ NX,NY

Set the CCD image size to nx, ny pixels. Note that the image size
must be a multiple of 4.

\SPEED\ KHZ

Set the camera speed in KHz. A list of valid speeds can be found in
the pull-down list in  Resolve3D's program window.

\STATS\ [ON | OFF]

Switch on or off the calculation of intensity statistics after image
acquisition. The default is ON.

\TLAPSE\ SECS

Wait until the specified number of seconds have elapsed since the
last time TLAPSE was used.  If more time has passed, then the wait
time is zero. See also WAIT and UWAIT.

\TTL\ CHANNELNUMBER [, On | Off,][DURATION_MSEC]

Trigger a TTL signal on the specified channel. If ONOFF is not 
specified, On is assumed, if DURATION_MSEC is not specified, a value
of 50 (msec) is used by default.

\ULTFOCUS\ [Calibrate | Measure |
            Maintain[,move_threshold][,max_iter][,iter_threshold] |
            CalibrateLUT | EnableLUT | MeasureLUT | MoveLUT ]

Use the UltimateFocus system for hardware-based autofocus
assistance.  The system utilizes two basic methods: A short-range
interpolated method used when the system is likely to be very near
focus and a  long-range (Look-Up Table based) method when the system
is likely to be farther out of focus. The long-range method is
primarily used in microtiter plate scanning.

Short-Range Focus Maintenance Commands:
  
  Calibrate: When at the plane of best focus in the sample, issuing 
             this command indicates to the system that the current Z
             is the focus (set point) to maintain.
  Measure:   Measure the difference between the calibrated set point
             and the current Z. Does not perform a move.
  Maintain:  Measure the current Z against the calibrated set point 
             and move if the limiting criteria are met:
               move_threshold: Only move if the difference is greater
                               than this value (microns)
               max_iter:       Allow this number of measure/move 
                               iterations to stay within 
                               move_threshold.
               iter_threshold: Only perform an iteration if the 
                               current difference is greater than 
                               this value. Normally the same as 
                               move_threshold.

Long-Range Focus Maintenance Commands:

  CalibrateLUT: Perform a lookup table calibration for the current
                combination of lens, polychroic, and plate type.
  EnableLUT:    Tells the system to find and engage the appropriate
                calibration lookup table for the current combination 
                of lens, polychroic, and plate type.
  MeasureLUT:   Measure and report the difference between the current
                stage Z and the calibrated set point.
  MoveLUT:      Measure and move from the current to desired set 
                point according to the calibrated lookup table.
                

\UPDATECAL\

Update the calibration table selection.

\USEBANK\ [N]

Change to bank number N, in the active window. See the USEWAVE
command.

\USE_BEAM_CONDITIONER\ True | False

Switch the use of the beam conditioner (cell viability filter) On or
Off. The beam conditioner is designed to block the effects of UV for
live-cell imaging. 

\USECAL\ TABLENAME

Switch to the calibration file named tablename.

\USECAM\ N

Switch to camera number N.


\USEWAVE\ [N]

Change to wave number N, in the active window.  Valid values of N are
1-3.

\USEWIN\ [N]

Switch to display window N.  If N is not specified, Resolve3D will
attempt to open a new window.

\UWAIT\ MICROSECONDS

Pause for the specified number of microseconds.  See also TLAPSE and
WAIT.

\VERBOSE\ [ON | OFF]

Report as much information as possible about Resolve3D's actions
through the status window.

\VISIT\ N

Move the XY or XYZ stage to point number N. See also RECORD.

\WAIT\ SECONDS

Pause for the specified number of seconds. See also TLAPSE and UWAIT.

\WRT\

Write the most recently acquired image  to the current image file and
then update the header. See also OPF, WRTF, and CLF.

\WRT2\

Write the most recently acquired image  to the current image file and
then  update the header.  Use with multi-point macros. See also
FIRSTPOINT, NEXTPOINT, POINTLIST, OPF2, WRT2F, and CLF2.

\WRTF\

Write the most recently acquired image  to the current image file.  
Similar to WRT, but faster because the header is not updated. See
also OPF, WRT, and CLF.

\WRT2F\

Write the most recently acquired image  to the current image file. 
Use with  multi-point macros. Similar to WRT2, but faster because the
header is not updated. See also FIRSTPOINT, NEXTPOINT, POINTLIST,
OPF2, WRT2, and CLF2.

\WRT_HDRS\

Commit the changes to all open image files to disk. This can be used
selectively with the WRTF and WRT2F commands to ensure that the image
file is up-to-date at certain times during data acquisition. 

\XSTEP\ STEPSIZE

Set the X step size in microns.

\YSTEP\ STEPSIZE

Set the Y step size in microns.

\ZSTEP\ STEPSIZE

Set the Z step size in microns.
