Sample Holder

Sample Holder >

Define Slide

Specifies the dimensions of a slide including its working area.

Used whenever slide is used as a sample holder.

Requires:

Module:

Stage XY axis

If you use a standardized slide, click Select from DB... and search for your slide in the slide database.

For non-standard slides, click Custom Slide... and define its properties (width, height). If you use slides with alignment crosses, it is recommended to check Alignment Crosses and set their X and Y Offset for later precise alignment.

Once you have selected/defined your slide, you have to specify its orientation on the stage. The orientation can be defined by Label Area Position, Smear Direction or Crosses Position. Select the real Orientation of the slide from the combo box.

At last it is possible to limit working area of the slide. This area can be a Rectangle or a Circle defined by Dimensions or using the Interactive feature which requires to Add XY points lying on the border of the selected shape (3 corner points for the rectangle or 3 edge points for the circle).

After defining the slide it is ready for alignment. Please see: Sample Holder > Align Slide Holder .

Sample Holder >

Define Stage Area

In this task you can specify the area of interest on your stage holder.

Used to define a non-standard sample holder.

Requires:

Module:

Stage XY axis

Name

Type the name of your stage area task.

Shape

Choose a stage area shape for its definition. Then click the arrows on the right side one after another while moving the stage to define the edge points. A small preview image is assigned to each defined point. Define without Capturing sets the scanned area shape without capturing images of the definition points, therefore no preview images are shown. Reset can be used to remove all defined points and start all over again.

Some shapes do not use edge buttons but a definition table - in such case use Add to enter the definition points.

Circle by radius shape requires to enter a Radius value and to Set Center Position.

Sample Holder >

Align Slide Holder

Determines exact position of the selected slide on the XY stage.

Used each time the slide is changed on the stage.

Requires:

Task:

Sample Holder > Define Slide

Module:

Stage XY axis

Select a slide from the combo box, move your stage to one corner of your slide and click Add. Move the stage to the Opposite Corner and click Add. Alignment is now finished. Changes to the alignment can be done by removing the XY coordinates clicking Remove or Remove All.

Name

Name of the Align Slide task.

Slide

Select slide for alignment.

Add

Uses the stage coordinates as corner points used for alignment of the slide.

Remove

Removes the selected coordinate.

Remove All

Removes all coordinates used for slide alignment.

Note

Slides can also be aligned globally using HCA/JOBS > Slide Holder > Align Slide Holder . This alignment is saved into the database and applied on new slides automatically.

Slides with covered corners
If your slide is mounted to the stage in a manner that its corner(s) are not visible in the Live View, it is impossible to align it using the predefined slides from the database. In this scenario there are two options:

Create a custom slide (using Sample Holder > Define Slide ) with Alignment Crosses and use these crosses to target corners of the coverslip, visible corners of the slide or any other reference points.
Use Sample Holder > Define Stage Area with a rectangular shape and find corners of the coverslip, visible corners of the slide or any other visible reference points.

Sample Holder >

Slide Loader

Communicates with the slide loader connected to your system.

Put this task to wizard to initialize the slide loader and scan hotels for slides just before the experiment begins.

Requires:

Device:

Slide loader

Module:

Stage XY axis

Click Initialize and follow the instructions to initialize your slide loader.
Scan for the loader hotels by clicking Scan Hotels.
To change the slide model used in the slide loader, click Select slide....
Select or deselect the found slides and hotels to be used in your job.
Optionally add the name and barcode to each of your slides and add Notes for the hotel.

Dialog Window Options

Slide loader name

Name of the task.

Initialize

(Re)initializes the connected slide loader.

Scan Hotels

Scans the hotels of the connected slide loader for all available slides.

Refresh

Refreshes the slide loader.

Select slide

Opens a dialog window defining the slide model used in the slide loader.

Hotel tabs

Each hotel tab represents a hotel of the connected slide loader. Slides contained in the selected hotel are listed below. The slides and hotels with a selected check box are used throughout the job.

Select All

Selects all slides in the hotel.

Clear Selection

Deselects any checked slides in the hotel.

Slide #

Position of the slide in the hotel.

Name

Name of the slide.

Barcode

Barcode of the slide.

Notes for

More notes for the selected slide.

Sample Holder >

Manual Slide List

Specifies the list of slides to be used in a loop over slides. These slides have to be changed manually.

Assign names and barcodes to slides in an ordered list. This information will be included in the experiment results.

Requires:

Task:

Sample Holder > Define Slide

Module:

Stage XY axis

Manual Slide List Name

Name of your manual slide list.

Slide Definition

Select the slide definition (Sample Holder > Define Slide ).

Multi Slide Holder

If using a multi slide holder, you can adjust the slide XY offset from the first slide in the table.

First Slide is Already on Stage

Check this option if your first slide is already on stage.

Add New Slide

Adds a new slide into the table.

Remove

Removes the selected slides.

Remove All

Removes all slides from the table.

Slide #

Automatic sequence number of your slides.

Name

Name of your single slides.

Barcode

Here you can enter your own barcoding for each slide.

X Offset from Slide #1

X axis offset from slide 1.

Y Offset from Slide #1

Y axis offset from slide 1.

Notes for

In the blank window below the slide ordered list you can fill out any other information about each of your currently selected slides.

Sample Holder >

Loop over Slides

Runs the contained tasks on each slide of the specified slide list.

Analyze all slides in the list and perform high-magnification capture on the ones meeting the defined condition.

Requires:

Task:

Sample Holder > Manual Slide List or Sample Holder > Slide Loader

Module:

Stage XY axis

Loop

Name your slide loop.

over

Choose a slide list from your current job.

Sample Holder >

Advanced Loop over Slides

This task can be used to fully control the procedure when working with a slide loader. Objective clearance (escape Autofocus + Focus Surface > Escape Z and refocus Autofocus + Focus Surface > Refocus Z ) has to be respected, otherwise the loop fails. The slides are loaded (Sample Holder > Load Slide to Stage ) and unloaded (Sample Holder > Unload Slide from Stage ) manually using the tasks.

Typically the job runs through all slides in the loader and assigns some information to them. For example, an analysis (Analysis > General Analysis ) can determine which slides are worth a high resolution capture - all slides are captured with low resolution and only those marked by the analysis are captured in high resolution.