# Applied Scientific Instrumentation

### Products

 Custom Optics diSPIM FTP FW1000: Filter Wheel MPPI MS2000, MFC2000 and RM2000 Controller Piezo Systems RAMM, MIM and VTS Portal Serial Command Software TG-1000/Tiger Controller Tracking & Stabilization XY Stage Z-Drive and Focus Stage

commands:scanr

# Command:SCANR (NR)

MS2000 or RM2000 syntax
Shortcut NR SCANR [X=start] [Y=stop] [Z=enc_divide] [F= #_pixels] X and Y in mm, Z and F as integer Using SS Z SCAN
Tiger micro-mirror syntax
Shortcut NR [addr#]SCANR [X=scans_per_slice] [Y=slices_per_volume] [Z=SPIM_mode] [F=volume_repeats] [R=slice_repeats] Integer Card-Addressed Using [addr#]SS Z MM_SPIM

Sets up the high-level operation of the SPIM state machine coordinated by the Micro-mirror card

scans_per_slice (X): sets the number of one-way beam scans in each slice (recall the slice corresponds to one image). Minimum value is 1.

slices_per_volume (Y): sets the number of slices (or images) in each volume. No facility exists to make it different for the two sides, though in principle it is possible. Minimum value is 1.

SPIM_mode (Z): sets a byte (by assigning a decimal) with the functions below. The default value is 2 (usual diSPIM, no special functionality).

• 2 LSBs correspond to single-sided vs. double-sided and the specified start side according to the following
• 3 for diSPIM starting on opposite side
• 2 for usual diSPIM (default)
• 1 for usual iSPIM
• 0 for iSPIM on opposite side
• Bits 2-3 were laser output mode in v2.85-v2.87; for v2.88+ this functionality is instead controlled by LED Z laser mode, bits 0-2.
• Bit 2 is set to disable micro-mirror moving to home position when other side is active during the SPIM state machine (i.e. rely completely on laser-based blanking while reducing micro-mirror movements). Default is unset (home move enabled). (v2.89+)
• Bit 3 is set to disable piezo moving to illumination position (home). Default is unset (piezo home enabled). (v2.89+)
• Bit 4 is set to alternate sides after each piezo/slice position (for interleaved stage scan). Note that piezo trigger signals will continue, but this is OK for the stage scan situation when the piezos’ SAA value is 0 and either the piezo’s SAO position is the same as the offset or else bit 3 is set. Default is unset (not alternating sides). (v3.09+).
• Bit 5 is set to alternate the beam scan direction between sweeps (either between slices or within same slice if the number of line scans per slice is more than 1). Default is unset (not alternating direction). Before v3.14 this was set using the LSB of the SAP setting. (v3.14+).
• Planned but not yet implemented: Bit 6 is set to add one extra camera trigger at the end of each side. Use this to accommodate “synchronous” or “overlap” camera mode without requiring an entire additional slice. Default is unset (no extra camera trigger). Proper operation requires the side delay (NV Y) be longer than the sum of the camera delay (NV T) and the camera duration (RT T). Because this occurs during the side switch time the total acquisition time is only increased by the time required for the final camera trigger.
• Bit 7 is reserved for future use

volume_repeats (F): sets the number of volumes to be collected per trigger event (two sides count as a single volume). Minimum value is 1.

Tiger (motorized) syntax
Shortcut NR [addr#]SCANR [X=start] [Y=stop] [Z=enc_divide] [F= #_pixels] [R=retrace_speed] X and Y in mm, Z and F as integer, R as percentage (0-100) Card-Addressed Using [addr#]SS Z SCAN

Sets up raster scan start and stop positions, with the position values expressed in millimeters. During scanning, the stage will move past both of these positions slightly, so that when scanning within the range specified, the scan proceeds with uniform speed (set by the SPEED command). On units equipped with hardware position Sync, the output pulse goes high as the stage crosses the start position.

On systems with the ENC_INT firmware module, an output pulse will occur every enc_divide number of encoder counts.

If the user specifies the #_pixels, the stop position will be calculated based upon the enc_divide and start position. Applicable to ENC_INT only.

On TG-1000 v3.30 and later use retrace_speed to specify the speed of the retrace move as a percentage of the max speed (decimal value between 0 and 100). The default value of 67 was the hardcoded value previously. This feature can be added to MS-2000 on customer request.

Address: 29391 W Enid Rd. Eugene, OR 97402, USA | Phone: +1 (541) 461-8181
commands/scanr.txt · Last modified: 2021/09/23 17:16 (external edit)