Stage XY Points

Stage XY Points >

Generate Points

Creates a pattern of XY points on the selected sample.

Used with quantitative/statistical methods to detect objects in a large number of “randomly” scanned frames.

Requires:

Task:

Well Plates > Loop over Wells or Sample Holder > Define Slide or Sample Holder > Define Stage Area

Module:

Stage XY axis

Main settings of this task are described below, however some settings allow for advanced adjustments (e.g. size, distance, count, ...). These functions are self-explanatory and are clearly depicted in the preview area.

Point Set Name

Type the name of your point set.

Select on which sample holder to generate the points.

Working area

Define the working area of the sample holder.

Field Size

Actual at Run-time uses the field of the currently used objective. Points are generated using the objective set right before the job run. Custom can be used to select a specific objective from the combo box which is then always used for the point generation. If a Acquisition > Triggered Experiment task is defined, its field size can be selected here.

Customize Preview Field Size

If checked, an objective can be selected from the drop-down menu defining the used field size.

Objective

Objective to be used for generating points.

Camera

If multiple cameras are connected, select the one to be used with this task.

Area Restriction

Specify the restriction inside the working area.

Point Placement

Choose one of the point placement methods listed. Manual method enables the user to add points by clicking into the preview area. Created points can be moved using the primary mouse button. Right-clicking deletes the point below the cursor.

Scan Direction

If Point Placement is set to Random, Random + Center or Manual, Random scan direction scans in the randomized order whereas Optimal Path scans points in the most effective order.

If Covering or Regular Pattern point placement is selected, Meander scans in a winding manner and Left to Right scans row by row from left to right.

If Point Placement is set to Spiral, options in the Scan Direction combo box specify the direction of rotation - clockwise (CW) / counterclockwise (CCW) and heading from/to the center (Outwards / Inwards).

Frames on Border

Specify whether the frames on the border of the restriction area are touching the border, completely inside or having a center inside.

Overlap

In Covering mode you can select the frame Overlap amount in percent.

For well plate loops, check the Auto option to set the optimal overlap to cover the rectangle inside the well automatically. To maximize the coverage to the edge of the well, combine the Auto option with the Frame inside option.

Count

Set the number of points you want to generate. The maximum number is indicated in the bracket.

Distribution

Uniform in Area places points evenly and Uniform in Radius places most of the points into the center of the restriction area.

Always Create New Points

There is always a new point set generated whenever the task is performed.

Randomize

Regenerates your random points.

Stage XY Points >

Predefined Points

Specifies a list of XY points on the selected sample manually in a tabular way.

Used for fixed samples. Find interesting scenes with a joystick and add them to the table one-by-one.

Requires:

Task:

Well Plates > Loop over Wells or Sample Holder > Define Slide or Sample Holder > Define Stage Area

Module:

Stage XY axis

Please see Multi-point Acquisition for details about points predefining. There are some additional options available within the JOBs module:

Include Z-Stack

Displays the Z-Stack definition column with the Z-stack definition button enabling to define a Z-Stack for the currently selected point.

Include Camera Settings

Displays the Camera column with the Redefine Camera Setting button enabling to adjust the camera settings (please see: Optical Configurations > Adjust Camera Settings Manually in OC ).

Include ROIs Definition

Displays the ROIs column with the button. Click this button and draw ROI(s) for the selected multi-point.

Include Labels

Labels defined in Well Plates > Label Well Plate task can be assigned to each multi-point. Select a label from the pull-down menu in the Label column.

Define Stimulation Laser Powers

If checked a dialog window appears when drawing stimulation ROIs. This window defines the power of each laser line on each stimulation group. Each point from a MultiPoint experiment can carry a different definition of ROIs or laser lines and laser powers.

Clear ROI(s) before Definition

Any previously drawn stimulation ROIs (drawn by clicking Draw ROI(s) or during Runtime) are cleared if this option is checked.

Note

The maximum number of generated points is limited to 30 000. For random points this limit is set to 1500. If you need to change this limit, run a job with the Stage XY Points > Predefined Points task, then open the Windows Registry Editor, search (Ctrl + F) one of the following functions: GeneratePoints_MaxPointCount

GeneratePoints_MaxRandomPointCount

and modify the “esrData” decimal value to a new value. Then click OK.

Stage XY Points >

New Point Set

Creates an empty point set. Points shall be added to it later either by Stage XY Points > Add Point to Point Set or Stage XY Points > Add/Edit Points Manually .

While looping an existing generated point set, only interesting scenes are added to the empty point set for later use.

Requires:

Module:

Stage XY axis

Point Set

Name your point set.

Stage XY Points >

Loop over Points

Runs the contained tasks on each XY point of the selected point set.

Used for capturing XY(Z) nd2 files.

Requires:

Task:

Stage XY Points > New Point Set or Stage XY Points > Predefined Points or Stage XY Points > Generate Points

Module:

Stage XY axis

Loop

Name your point loop.

over

Select one of your active point tasks to be looped (Stage XY Points > Generate Points , Stage XY Points > Predefined Points , Stage XY Points > New Point Set ).

Split storage per point

This option influences how the system stores the captured data on the disk. If checked, separate ND2 file will be created for each point.

Move to XY

If checked, the stage is moved to the XY points.

Move to Z

If checked, the Z-drive moves to the Z position assigned to the current well (e.g. Z value found by Autofocus + Focus Surface > Autofocus during the first Well Plates > Loop over Wells ).

Advanced

Each point can be assigned to a class (by an expression). If you select this option, the Loop over wells in class field appears. Type the class number to which the current loop will be applied.

Use Point PFS Offset

These options tells the system to set Z drive to a position previously assigned to the current point.

Use Points with

If you select a label defined by the System > Create Labels task, the tasks inside Loop over Points will be executed only on points marked with this label.

Stage XY Points >

Move to Point

This task can be used inside a point loop to move to a XY/Z position of a point.

If a condition is met, move the motorized stage to a specific point.

Requires:

Task:

Stage XY Points > Loop over Points

Module:

Stage XY axis

Move to

Defines in which point loop the movement will be performed.

Move to XY

Moves to the XY coordinates of the point.

Move to Z

Moves to the Z coordinate of the point.

Use Well PFS Offset

PFS Offset of the well is incorporated into the movement.

Stage XY Points >

Move to Previous/Next Point

Moves the XY stage to the previous/next well.

When placed in runtime, the user can move to the previous/next point to check the procedure.

Requires:

Task:

Stage XY Points > Loop over Points

Module:

Stage XY axis

Task name

Name of your task.

Move from

Select the point from which you want to move.

Specify the moving distance to the previous/next point.

Previous, Next

Choose the point direction you want to move.

Stage XY Points >

Offset Point Set

This task can correct the XY offset between objectives.

Used to offset all XYZ coordinates of the current stage position or of the selected point set.

Requires:

Module:

Stage XY axis

X, Y, Z shift

Name of the task.

Is used to select a point set (Stage XY Points > Generate Points , Stage XY Points > Predefined Points , Stage XY Points > New Point Set ) or the Actual Stage Position to be shifted.

Correct XY Offset between Objectives

If checked, XY correction between objectives is performed using the two objectives specified below. Please see Devices > Objectives XY Offset Setup for more information.

Define Offset Manually

Specify distances of the manual shift in all three axes (X, Y, Z).

Stage XY Points >

Add Point to Point Set

Adds a named XY point to the selected point set. Current XY position is used.

Pause the job to manually find an interesting XY position using the joystick and include this point in the analysis.

Requires:

Task:

Stage XY Points > Predefined Points

Module:

Stage XY axis

Name

Name your new point.

Add current stage point to

Select a point set to which you want to add a new stage point.

Stage XY Points >

Remove Point from Point Set

Removes the current XY point from the selected point set which is used in a point loop.

Use this task in an XY point loop to remove points which are not useful for further analysis (e.g. do not produce any image signal).

Requires:

Task:

Stage XY Points > Loop over Points

Module:

Stage XY axis

Remove Point from Point Set

Select an active point loop from which your point will be removed.

Stage XY Points >

Add/Edit Points Manually

Waits for the user to add or edit points to the selected point set manually during the runtime.

May be used to check focus and offset the point set if needed.

Requires:

Task:

Stage XY Points > Predefined Points

Module:

Stage XY axis

Name

Enter the name of your manually defined points.

Embed to progress window

Check this function if you want to embed the Edit Points window into the bottom of the Job Execution Progress window.

Point set

Select a point set which you want to edit manually.

Stage XY Points >

Append Point Set to Point Set

Appends points from a selected point list into another selected point list.

Append interesting points to a list on which a high magnification capture will be made.

Requires:

Task:

Stage XY Points > Predefined Points or Stage XY Points > Generate Points

Module:

Stage XY axis

Name

Name of your task.

Append all points from

All points from this list will be appended.

Defines to which point list will the points selected from the first combo box be appended.

Stage XY Points >

Clear Point Set

Removes all points from the selected point list.

If the user decides to clear the point list e.g. because of an incorrect sample.

Requires:

Task:

Stage XY Points > Predefined Points or Stage XY Points > Generate Points

Module:

Stage XY axis

Name

Name of your task.

Remove all points from

Select the plate list which will be cleared.

Stage XY Points >

Export Point Set to ND

Exports the selected point set definition to the ND Acquisition window.

Find points of interest using a complex job and use them later in ND Acquisition.

Requires:

Task:

Stage XY Points > Predefined Points or Stage XY Points > New Point Set

Module:

Stage XY axis

Point set to export

Select the point set you want to export to the XY tab of the ND Acquisition window.

Append points

Adds new generated points to the the XY tab of the ND Acquisition window right behind already existing points.

Replace points

Replaces all existing points in the XY tab of the ND Acquisition window by newly generated points.

Stage XY Points >

Reorder Point Set

Reorders the input point set to minimize the distance between the points.

Use this task to optimize the point trajectory.

Requires:

Task:

Stage XY Points > New Point Set or Stage XY Points > Predefined Points or Stage XY Points > Generate Points

Module:

Stage XY axis

Stage XY Points >

Import Point Set from ND

Imports the multi point definition from the ND Acquisition window to the selected point set. The existing point set settings will be overwritten.

Use the multi points created in ND Acquisition to run a complex job.

Requires:

Task:

Stage XY Points > Predefined Points or Stage XY Points > New Point Set

Module:

Stage XY axis

Import to point set

Select a point set to which data from the ND Acquisition window will be imported.

Append points

Adds newly generated points to your selected point set behind already existing points.

Replace points

Replaces all existing points in your point set by newly generated points.

Stage XY Points >

Get Current XY Position

Retrieves the current XY position of the stage device.

Use the retrieved XY value to move the stage to this position later on in the job.

Requires:

Module:

Stage XY axis

Stage XY Points >

Move to XY Position

Moves the stage to the previously remembered position.

Use the retrieved XY value to move the stage to this position later on in the job.

Requires:

Task:

Stage XY Points > Get Current XY Position

Module:

Stage XY axis

Stage XY Points >

Set XY Speed/Accuracy

Sets the stage speed so that different speeds can be used throughout the job.

Use a slower stage speed to prevent the sample shift and get stability for the PFS during acquisition. Then use faster speed when changing samples to reduce the total acquisition time.

Requires:

Module:

Stage XY axis

Name

Name of your task.

XY Speed

Select the check box and enter a new speed value of the stage. Otherwise the default value will be used.

Accuracy

Select the check box and select a different value to be used. Better accuracy (lower value) usually results in longer movement times. If you select the Open value, the stage position will not be corrected at all. It is the fastest but least precise option.

Restore original values when the job finishes

If selected, default speed and accuracy values are set after the job is finished.

Stage XY Points >