X-Y Stage Reference Manual

Transcription

1 X-Y Stage Reference Manual Improvision, Viscount Centre II, University of Warwick Science Park, Millburn Hill Road, Coventry. CV4 7HS Tel: 0044 (0) Fax: 0044 (0) Internet:

2 Printing History Edition Date Edition 1 September 1998 Improvision believes the information in this manual to be correct at the date of issue. However, it is subject to change at any time and does not represent a commitment on the part of Improvision. Improvision shall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing, performance, or use of this manual. Improvision has a policy of continual development and reserves the right to change information within this manual without notice to reflect changes in the systemõs design and specification Improvision, Image Processing & Vision Company Limited. All rights reserved. Copyright Notice Apple, Finder and Macintosh are registered trademarks of Apple Computer, Inc. Other brand or product names are the trademarks of their respective holders.

3 X-Y STAGE Controlling the X-Y Stage Overview This module allows you to control an X-Y stage remotely from your computer. Refer to Improvision for details of devices that are currently supported. The X-Y stage module is not part of the core product, but may be purchased separately. The module provides: A palette which contains the joystick control for the X-Y stage, a view of the stage and work area and various menus, including a Control menu with calibration and safe motion commands. A Stage Manager window which gives you a larger, scrollable view of the stage area and the work area, and a wider range of commands. For example, there are various commands for setting up and editing stored points to which you can move the X-Y stage. In many instances, you can perform tasks from either the Palette or the Stage Manager window. This chapter describes the X-Y Stage Window and Palette and how to use them. Refer to the Serial Devices Reference Guide for further details on connecting the X-Y stage to the Macintosh, and setting the Serial Port Preferences. If you are using a Ludl controller, refer to the Serial Devices Reference Guide for information about setting Ludl preferences. Contents Overview...1 Safety Issues...2 X-Y Stage Window...2 Getting Ready to Use the Stage...3 Creating Stored Points...4 Stage Manager Window Menus...8 X-Y Stage Palette...10 X-Y Stage and Automator tasks...12 X-Y Stage 1

4 OPENLAB Safety Issues When you calibrate or move the X-Y stage, you must make sure that the lens of your microscope or focus drive is safely out of the way. Openlab software provides several safety features. It allows you to set a Safe Position for your device and will move automatically to the safe position when calibrating. It also allows you to set the X-Y stage in a Safe Motion Mode so that your focus drive is retracted whenever you move the stage. X-Y Stage Window You can display the X-Y Stage Window by: Selecting X-Y Stage from the Openlab Windows menu. Selecting Stage Manager on the Palette s Controls menu. The X-Y Stage window provides you with a large, scrollable view of the stage and work area. You use the menus on this window to create and maintain stored points, to set up the work area, put the drive into safe motion mode and calibrate the X-Y stage. You can also use the menus to move the X-Y stage to a stored point, and to control how points are displayed in the points list. Stage Manager menus Current position of stage Work area Stage area List of stored points Use the scroll bars to view more of the window Click and drag to expand or contract the window 2 Openlab v.2

5 X-Y STAGE Getting Ready to Use the Stage We recommend that you carry out the following tasks, before you start to work with the stage for the first time: Put the drive into a safe position and calibrate the X-Y stage. Define your work area. Create stored points, as appropriate, and use the View menu commands to adjust how the points are sorted and displayed. If your device supports it, set the Enforce Limits command. If appropriate, enable the Safe Motion Mode. You are now ready to use the X-Y Stage palette. See page 10. Calibrating the Stage 1. Make sure that the microscope lens is in a safe position. (Enable Safe Motion Mode from the Work Area menu.) 2. Select Calibrate Stage... from the Work Area menu. 3. Check that the objective lens is in a safe position and click on OK. During calibration, the stepper motor drives the X-Y stage across the whole stage area until the limit switches click off. X-Y Stage 3

6 OPENLAB Setting Up the Work Area 1. Make sure that both the Palette and the Stage Manager windows are displayed. 2. Use the joystick on the palette to move the pointer to the start point of the work area - this is the top left-hand corner. The display on the palette will show you the current position in calibrated units Select Set Top Left from the Work Area menu. Now use the joystick to move the pointer to the end point of the work area - this is the bottom right-hand corner. The display on the palette will show you the current position in calibrated units. Select Set Bottom Right from the Work Area menu. Note: As an alternative to using the joystick, you could also use the New... command from the Points menu to create stored points for the top left and bottom right positions, then use the Go and Set Top Left, Set Bottom Right commands to define the work area. Creating Stored Points There are three ways of creating a stored point: Use the Points menu on the Stage Manager window. You can then define the exact location of the stored point(s). Move the pointer to the appropriate position in the current window and press the space bar. This creates a single, stored point at the pointer position. Move the pointer to the appropriate position press the icon on the palette. This creates a single, stored point at the pointer position. Defining Points You can define the exact location for a new point, or you can use the AutoPlace... command to distribute a number of points automatically over the work or stage area. 4 Openlab v.2

7 X-Y STAGE To create a new point 1. Select New... from the Points menu. 2. Enter a name for the point in the Add a point called: box. This name will appear on the Stage Manager window and the palette Enter the exact co-ordinates in the X and Y boxes. Click on the appropriate icon to select a style: for the point. Select a colour from the pop-up list. Click on OK. To distribute new points automatically 1. Select Auto Place... from the Points menu. X-Y Stage 5

8 OPENLAB Decide how many points you want to create and enter the number in the Place box. Enter an overall name for the points in the new points named box. Openlab will use this name as the stem for all the points, and will just add a number to identify individual points in the auto place sequence. 4. Decide how you want the points to be distributed: Click on Randomly or on Evenly Distributed. Click on Over Stage Area or on Within Working Area Click on the appropriate icon to select a style: for the point. Select a colour from the pop-up list. Click on OK. In the following example, we have created four points automatically. They were distributed randomly across the full stage area. Note: Point 2 is not visible on the Stage Manager window because we have used the Hide selected points command to hide it. See next section. 6 Openlab v.2

9 X-Y STAGE Maintaining points Once you have created points, you can use commands from the Stage Manager menus to: Edit the point Delete selected point(s) Hide or display selected point(s) Control the sort order for points in the points list To edit a point Select the point by clicking on it in the Points list. Select Edit Selected Point... from the Points menu. 3. Edit any of the settings, as required and click on OK. To delete point(s) 1. Select the point(s) in the Points list 2. Select Delete Selected Points from the Points menu. 3. You will not be able to undo this action. If you want to delete all the selected points, click on OK. X-Y Stage 7

10 OPENLAB To hide or display point(s) Select the point(s) in the Points list in the Stage Manager Window. Select Hide Selected Points or Show Selected Points from the Points menu. When you hide points, they are removed from the work area/stage area window but they remain on the points list, in italics. To control sort order in points list Select the appropriate sort order from the View menu. Most of the options are selfexplanatory. If you enable Show Scanpath (so that it has a tick next to it), a line will be displayed between all the visible points, in the selected sort order. Ensuring Safe Motion There are two ways of ensuring safe motion. If your microscope supports it, enable Enforce Limits form the Work Area menu. This keeps the stage within the work area. Enable the Safe Motion Mode command. This retracts the focus drive, whenever you move the stage from point to point. Stage Manager Window Menus Points Menu To create a new stored point To distribute a number of new stored points automatically To delete selected stored points To edit a selected stored point To show/hide stored points in the Stage Manager window 8 Openlab v.2

11 X-Y STAGE View Menu Select a sort order for the points list Hides/shows the grid in the window Hides/shows a line between the visible points in the selected sort order Scrolls the window so that you can see the current position of the stage Work Area menu To set the top left point of the work area To set the bottom right point of the work area To undo the last change To reset the work area to the whole stage area To drive the stage back within the work area To make the stage stay within the work area To calibrate the stage To enable/disable safe motion mode Go Menu Select a stored point to move the stage directly to that point A indicates the stage is currently at that point A indicates the stage is close to that point Italics mean the point is outside the work area X-Y Stage 9

12 OPENLAB X-Y Stage Palette Once you have set the work area and calibration, you can use the palette to control the X-Y stage. Click and drag the joystick in the direction that you want to move the stage. Use the Go menu commands to move to a stored point. The Control menu provides access to the calibration and safe motion mode commands. Menus Stored point The red cross indicates the current position The current position in calibrated units Click and drag joystick in the direction you want to move the stage Click here to create a new stored point at the current position Note: The window above the joystick represents the stage area and work area. You get a larger, scrollable view of this area in the Stage Manager window. Ludl Devices 10 Openlab v.2 If the X-Y stage continues to move when you release the joystick, you need to upgrade your Ludl firmware. Alternatively, you can disable smooth movement in the Ludl preferences. See the separate document, Serial Devices Reference Guide, for further information.

13 X-Y STAGE Palette Menus There are three menus on the X-Y Stage Palette: Device Menu You may have more than one X-Y stage. Select the required device from the Device pop-up menu. A tick appears next to the selected device. The name of the selected device will also appear at the bottom of the X-Y Stage Palette. Note: If you have a Ludl controller and no X-Y stage attached, set the Device to None. If you do not, the Ludl controller will search constantly for the X-Y stage, and this will slow down system performance. (Alternatively, move the X-Y Stage module out of the active modules folder.) Control Menu This menu provides a number of control commands: Calibrate... displays the Calibrate dialogue which is described on page 3. Safe Motion Mode which enables safe motion for use with focus drives. If this mode is set (it has a tick next to it), the drive will retract whenever you move the stage. This is useful if your experiment requires you to move between a number of positions and samples. Stage Manager displays the Stage Manager window, which is described on page 2. Go Menu The commands on this menu allow you to move the stage to a stored point. A tick next to the point name indicates that the stage is currently at that point. A _ next to the point name indicates that the stage is very close that point If the point name is in italics, it is outside the work area Stored points are normally created and maintained on the Stage Manager window, but you can also set a stored point at the current position on the Palette. Click on the icon. X-Y Stage 11

14 OPENLAB X-Y Stage and Automator tasks If you have the Automator module, you will be able to use X-Y Stage task in your automation. The task will appear in the Task List in the Automator Window. This section describes the X-Y Stage task. Refer to the Automator Reference Manual for further details about creating and running automations. 12 Openlab v.2

15 X-Y STAGE Move X-Y Stage This task moves the X-Y stage to a specified position when the task executes. Click on one of the buttons to select the type of position and then enter the appropriate position details. Select absolute position if you know the exact location and enter an expression for the exact co-ordinates in the X and the Y boxes. Select index position if you know the index value of the pixel and enter an expression for the indexed position. Select the position if you want to specify a Point by the number that you gave it in the Stage Manager and select the appropriate position number from the pop-up menu. Select the position named if you want to specify a Point by the name that you gave it in the Stage Manager and enter an expression for the position name. Click to select position option Select appropriate position details X-Y Stage 13

16 OPENLAB 14 Openlab v.2