Parameters describing hardware are always hidden from the calling application (and from the application developer) and typically hidden from the user. If needed, the user can access these parameters through the visual interface. The hardware is described by the following parameters. These parameters are kept in ASCII text files and loaded at startup of ScopeTool. The values in the parameter files correspond to a particular hardware configuration.
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XYCONTRX |
Name of controller for the X axis. |
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XYCONTRY |
Name of controller for the Y axis. |
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XYSCREWLEAD |
Lead of the leadscrews in the stage in mm. |
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XYMOTORSTEPS |
Number of steps per revolution of the stage motors. |
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XYSTEPDIVIDE |
Microstepping divide factor. One microstep = 1 / 2^XYSTEPDIVIDE of full step. |
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XYHOLDCURRENT |
Hold current in % of max. |
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XYRUNCURRENT |
Run current in % of max. |
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XYSLEWVELOCITY |
Slew velocity in microsteps per second. |
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XYINITVELOCITY |
Initial velocity in microsteps per second. |
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XYACCELERATION |
Acceleration in number of microsteps at each speed level. |
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XYDECELERATION |
Deceleration in number of microsteps at each speed level. |
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XYJOGSPEEDLOW |
Low jog speed from the switchstick in microsteps per second. |
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XYJOGSPEEDHIGH |
High jog speed from the switchstick in microsteps per second. |
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XYBACKLASHX |
Backlash in X axis in microns. |
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XYBACKLASHY |
Backlash in Y axis in microns. |
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XYHOMESPEED |
Speed for homing in microsteps per second. |
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XYMOVEOUT |
Reverse move before homing in microns. |
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XYJUMPSIZE |
Distance of stage jump from the interface in microns. |
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XYJOYMAXSPEED |
Maximum stage speed when controlled by the joystick in microsteps per second. |
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XYLIMPOLARITY |
Stage limit switches normally open (0) or normally closed (1). |
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ZCONTR |
Name of focus controller. |
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ZSTROKEPERROT |
Distance traveled by focus mechanism of the microscope per full rotation of the fine focus knob in mm. |
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ZMOTORSTEPS |
Number of steps per revolution of the focus motor. |
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ZSTEPDIVIDE |
Microstepping divide factor. One microstep = 1 / 2^ZSTEPDIVIDE of full step. |
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ZHOLDCURRENT |
Hold current in % of max. |
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ZRUNCURRENT |
Run current in % of max. |
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ZSLEWVELOCITY |
Slew velocity in microsteps per second. |
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ZINITVELOCITY |
Initial velocity in microsteps per second. |
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ZACCELERATION |
Acceleration in number of microsteps at each speed level. |
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ZDECELERATION |
Deceleration in number of microsteps at each speed level. |
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ZJOGSPEEDLOW |
Low jog speed from the switchstick in microsteps per second. |
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ZJOGSPEEDHIGH |
High jog speed from the switchstick in microsteps per second. |
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ZBACKLASH |
Backlash in the focusing mechanism of the microscope in microns. |
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ZJUMPSIZE |
Distance of focus jump from the interface in microns. |
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ZCOARSEFACTOR |
Ratio of coarse to fine focus step. |
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ZJOYMAXSPEED |
Maximum focus speed when controlled by the joystick in microsteps per second. |
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ZHOMESPEED |
Speed for homing in microsteps per second. |
Filter wheel F - ST_PARW1.TXT Tips on adjusting parameters
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W1CONTR |
Name of F wheel controller. |
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W1STEPDIVIDE |
Microstepping divide factor. One microstep = 1 / 2^W1STEPDIVIDE of full step. |
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W1HOLDCURRENT |
Hold current in % of max. |
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W1RUNCURRENT |
Run current in % of max. |
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W1SLEWVELOCITY |
Slew velocity in microsteps per second. |
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W1INITVELOCITY |
Initial velocity in microsteps per second. |
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W1ACCELERATION |
Acceleration in number of microsteps at each speed level. |
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W1DECELERATION |
Deceleration in number of microsteps at each speed level. |
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W1MSTEPSPERFILT |
Microsteps between adjacent filer positions. |
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W1OFFSETHOME |
Microsteps from physical home to filter 1. |
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W1FILTPOSITIONS |
Number of filter positions in the wheel. |
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W1HOMESPEED |
Speed for homing in microsteps per second. |
Filter wheel B - ST_PARW2.TXT
Filter wheel B has parameters similar to wheel F.
Joystick - ST_JOY.TXT
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JAXIS1_L |
Lowest reading from the joystick axis 1. |
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JAXIS1_0 |
Reading from the joystick axis 1 corresponding to the idle position. |
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JAXIS1_R |
Highest reading from the joystick axis 1. |
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JAXIS2_L |
Lowest reading from the joystick axis 2. |
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JAXIS2_0 |
Reading from the joystick axis 2 corresponding to the idle position. |
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JAXIS2_R |
Highest reading from the joystick axis 2. |
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JLATENT |
Percent of deflection of the joystick around the idle position which is treated as idle. This is needed to prevent spurious moves. |
Commands assigned to joystick - ST_JOYCMDS.TXT
The file ST_JOYCMDS.TXT contains 5 lines (for a 4-button mouse) with any ScopeTool commands. The command in the first line is executed upon startup. Other commands are assigned to buttons from 1 to 4 and are executed when corresponding button is pressed. Example: Joy WZ / Joy ToggleAxes / Scan FF / Scan NF / Scan PF/
Field of view - ST_FIELD.TXT
Size of the field of view depends on the microscope optics and whether this is the visual or camera field of view. All dimensions are in microns. These parameters must be calibrated by the user.
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FIELD10X |
Horizontal dimension of the field of view under magnification 10X. |
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FIELD10Y |
Vertical dimension of the field of view under magnification 10X. |
Specimen parameters - ST_SPECIMEN.TXT
The following parameters describe the location of the specimen (e.g., slide) in the coordinate system of the stage. Depending on the type of stage, these parameters may be calibrated at the factory or by the user. All dimensions are in microns.
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SPECIMENXE |
Horizontal dimension of the specimen in microns. |
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SPECIMENYE |
Vertical dimension of the specimen in microns. |
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SPECIMENX0 |
X coordinate of the top left corner of the specimen in the stage coordinate system in microns. |
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SPECIMENY0 |
Y coordinate of the top left corner of the specimen in the stage coordinate system in microns. |
Scan area parameters - ST_SCANAREA.TXT
The following parameters define the size and position of the scanning area. All dimensions are in microns. These parameters are recalculated when "Area Set" commands are executed.
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SCANAREAXE |
Horizontal dimension of the scan area in microns. |
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SCANAREAYE |
Vertical dimension of the scan area in microns. |
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SCANAREAX0 |
X coordinate of the top left corner of the scan area in the specimen coordinate system in microns. |
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SCANAREAY0 |
Y coordinate of the top left corner of the scan area in the specimen coordinate system in microns. |
Scan area parameters - ST_SCANGRID.TXT
The following parameters define the size and position of the scanning grid. All dimensions are in microns. These parameters are recalculated when "Grid" commands change them.
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GRIDSTEPX |
Step between the nodes in the grid in X direction in microns. |
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GRIDSTEPY |
Step between the nodes in the grid in Y direction in microns. |
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GRIDSITESX |
Number of nodes in the grid in Y direction. |
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GRIDSITESY |
Number of nodes in the grid in Y direction. |
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GRIDTLX |
X coordinate of the top left corner of the grid in the stage coordinate system in microns. |
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GRIDTLY |
Y coordinate of the top left corner of the grid in the stage coordinate system in microns. |
Scan parameters - ST_SCAN.TXT
The following parameters define the order in which fields of view will be visited during scanning.
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SCANTILEGRID |
Scan by tiling the scan area defined by ST_SCANAREA.TXT with fields of view defined by ST_FIELD.TXT (1), or by visiting nodes of a grid defined by ST_GRID.TXT (2) |
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SCANAXIS |
Scan along X axis (0), or along Y axis (1). |
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SCANDIRECTION |
From left to right or from top to bottom (0), from right to left or from bottom to top (1). |
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SCANOVERLAP |
Overlap of fields of view during scanning in microns. |
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SCANSTART |
Start scanning in the corner of the scan area (0), start scanning in the beginning of the middle row or column of the scan area (1). |
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SCANRESTRICTION |
Visit all scan fields (0), visit only fields within an oval, inscribed in the scan area (1), applicable to tile scanning only |
Focus Shift parameters - ST_DZWi-<objective name>.TXT, where i=1,2
These files describe the focus shift parameters between different filters in each filter wheel. There may be any number of these files, e.g. for each objective.
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W2DZ1 |
0 |
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W2DZ2 |
Shift in microns of the best focus for this filter relative to filter 1. |
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... |
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W2DZ<number of filters> |
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Objective and Magnification parameters - ST_OBJPOSMAG.TXT
The following parameters define which objectives are in which positions in the objective turret. They have the form:
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OBJPOSi |
Magnification |
Configuration parameters - ST_CONFIG.TXT
The following are general and configuration-dependent parameters.
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MPORT |
Serial port number to which motor controller unit is connected |
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PORTTIMEOUT |
Timeout for response from the motor controller in milliseconds |
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MOVETIMEOUT |
Timeout for completion of a move command in seconds |
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JOYSTARTON |
Joystick active on startup? 1-yes, 0-no. |
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XY_INSTALLED |
Stage installed? 1-yes, 0-no. |
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Z_INSTALLED |
Focus drive installed? 1-yes, 0-no. |
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W1_INSTALLED |
Filter wheel 1 (F) installed? 1-yes, 0-no. |
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W2_INSTALLED |
Filter wheel 2 (B) installed? 1-yes, 0-no. |
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