Roche BenchMark XT/LT User manual

VSS v12.5 1 1015672EN RevA

Ventana System Software

Version 12.5 Software Update

____________________________________________

Ventana Medical Systems, Inc.

www.ventana.com

Part No. 1015672EN Rev A

September 2016

VSS v12.5 2 1015672EN RevA

Ventana System Software Version 12.5 Software Update

Copyright

Trademark

BENCHMARK, DISCOVERY, VENTANA, and the VENTANA logo are trademarks of Roche. All other trademarks are

the property of their respective owners.

Licenses

VENTANA products may be governed by one or more license agreements including third-party licenses. Users of the

products or software discussed in this document, including Ventana System Software Version 12.5, and other VENTANA

products are subject to the terms of such licenses. Other products, components modules features and/or functions

referenced in this document that are not part of the BenchMark ULTRA base instrument or package of products discussed

herein may not be received or used by any person unless the relevant license fees are paid and the relevant license

agreements are duly executed.

Contact

Ventana Medical Systems, Inc.

a Member of the Roche Group

1910 E. Innovation Park Drive

Tucson, Arizona 85755

USA

+1 520 887-2155

+1 800 227-2155 (USA)

www.ventana.com

Roche Diagnostics GmbH

Sandhofer Strasse 116

D-68305 Mannheim

Germany

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Contents

Ventana System Software 6

System Information and Software Version Control 6

Global Navigation ................................................................................................6

Instrument Bar .....................................................................................................7

Communicator .....................................................................................................7

Home View ..........................................................................................................7

Instrument View ..................................................................................................8

Generate Slide Labels 9

Create a Slide Label .............................................................................................9

Create a Batch of Slide Labels ..........................................................................11

Print a Batch of Slide Labels .............................................................................11

Remove a Label from the Print List ..................................................................12

Cancel Slide Label Printing ...............................................................................12

Apply a Slide Label ...........................................................................................12

Print Labels from the Order List ........................................................................13

Perform a Staining Run 13

Running Mode ...................................................................................................13

Start the Staining Run ........................................................................................14

Print Run Reports ..............................................................................................14

Work With Slides 16

Edit Slide Data ...................................................................................................16

Manage Slide Orders 17

About the Order List ..........................................................................................17

Organize the Order List .....................................................................................19

Find Orders ........................................................................................................21

Print Orders ........................................................................................................22

View Order Details ............................................................................................22

Create a New Order ...........................................................................................22

Change Order Information ................................................................................23

Create Multiple Orders ......................................................................................24

Delete an Order ..................................................................................................27

Print Reports and Labels ....................................................................................27

Reports 29

Quality Control Reports .....................................................................................29

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Managing Inventory 33

Print a Detail Usage Report ...............................................................................33

Register a Ventana Reagent ..............................................................................35

Register Non-Ventana Products ........................................................................36

Log Products ......................................................................................................37

Fill a Ventana Dispenser ...................................................................................42

Deactivate Products ...........................................................................................46

Reactivate Products ...........................................................................................46

Create Staining Protocols 46

Create and Print a Protocol ................................................................................46

About Staining Protocols ...................................................................................48

Instrument Protocols Option .............................................................................48

Search, View, and Print Features in the Protocol Editor ...................................49

Selectable Protocol Options ..............................................................................50

Protocol Views ..................................................................................................50

How to Filter Protocols .....................................................................................52

How to Search Protocol Steps by Keyword ......................................................53

How to Print from the Protocol Editor ..............................................................53

How to Use the Zoom Feature ..........................................................................54

How to Scroll with the Mouse Wheel ...............................................................54

Modify a Protocol ..............................................................................................54

Delete a Protocol ...............................................................................................55

View Protocol Definitions .................................................................................55

Print Protocol Steps and Details ........................................................................55

Print a Protocol Usage Report ...........................................................................56

Set Up the System 56

Set Up the Host ..................................................................................................57

Specify SLS Options .........................................................................................59

Set Up Passwords and Log-ins ..........................................................................60

Add a User Name and Password .......................................................................61

Change a User Name and Password ..................................................................62

Delete a User Name and Password ....................................................................62

Add a User Group ..............................................................................................62

Change a User Group ........................................................................................63

Delete a User Group ..........................................................................................63

Look Up User Names or Groups .......................................................................63

Enter Address for Report Headings ...................................................................64

Find Hardware Serial Numbers .........................................................................64

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VENTANA Connect 64

Cleaning and Maintenance 65

Using the Clean Icon .........................................................................................65

Instrument Maintenance ....................................................................................66

Print User Maintenance Logs ............................................................................67

Record Completed Maintenance .......................................................................68

About Decontamination Tasks ..........................................................................68

View or Add Maintenance Notes ......................................................................68

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Ventana System Software

This portion of the operator’s manual is to assist users navigating Ventana System Software (VSS) who are

familiar with NexES software. This document provides details on performing tasks previously performed with

NexES software.

The Ventana System Software provides easy access to key functions and processing information. Three

features in the upper screen—the Global Navigation, Instrument Bar, and Communicator—are available

everywhere in the software. The Home View appears in the lower screen at startup. It provides System buttons

to navigate to other functions and shows images of connected instruments.

Some key software features are described in this section.

System Information and Software Version Control

In the Home View, you can click the System Info button to see the VSS Software part number and revision

number.

Figure 1. Software System Information

Global Navigation

Figure 2. Global Navigation

The Global Navigation bar is at the top of the screen. From anywhere in the system, the Global Navigation

icons go directly to: 1) Home View, 2) the Login window, 3) the Order List, where you can view and manage

orders and labels, and 4) the Inventory List, where you can view and manage products.

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Instrument Bar

The Instrument Bar is below the Global Navigation. It shows status information for each instrument connected

to the computer. Status is indicated by colored lights. When an instrument is connected and idle, its indicators

are green. During slide processing, indicators are yellow.

Figure 3. Instrument Bar

Communicator

The Communicator shows information and error messages for connected instruments. Each message is

associated with a timestamp and an icon representing the message type. For error messages, a Sign Off button

appears at the right of the panel. You can click the resize arrow to expand or shrink the message area. You can

also enter notes about a message.

Figure 4. Communicator

Home View

When the software starts up, the Home View appears in the lower part of the screen. It shows the same data as

the Instrument Bar, but in a graphic format. It also provides System buttons to navigate to other software

functions and an Instrument Setup button for navigating instruments. You can click the Home icon in the

Global Navigation to return to this view from anywhere in the system.

Figure 5. Home View

(1) Instrument status indicators.

(2) Next operator action.

(3) Time until next action.

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Instrument View

The Instrument View allows you to view the status of each subcomponent of a configured staining instrument

at a glance (reagent, slide, bulk, and waste), and allows navigation to detailed views of each subcomponent. To

navigate to an Instrument View, click the instrument name in the Instrument Bar or the instrument image in the

Home View.

Figure 6. Instrument View

Feature Descriptions at Instrument View

Feature Description

Instrument Home

icon

From other views accessed from Instrument View, returns you to the Instrument

View.

Reagent icon Opens the reagent histogram where you can see details for each dispenser on

the reagent carousel.

Slide icon Opens the slide histogram where you can see details for each slide position.

Instrument

Maintenance icon

Opens Instrument Maintenance where you can print maintenance logs and

check lists, record maintenance done, and run functions to decontaminate the

instrument or clean the slide drawers.

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Generate Slide Labels

Create a Slide Label

1. At the Home View, click the Create Label button.

Figure 7. Create Label Button

The SLS opens.

Clean icon Starts an instrument cleaning cycle with one mouse click.

Slide images Displays which slide positions are available and in use and the status of the

slides on the instrument.

Reagent wheel Displays which reagent slots are available and in use and the status of the

reagent dispensers on the instrument.

Reagent Grid icon Opens the reagent grid that displays recently scanned reagent information. You

also now have the ability to scan reagents on the instrument without having

started a run, to gather already loaded reagent information.

Instrument name Displays the instrument name and the next operator action.

Bulk bottles Monitor the status of bulk reagent bottles.

Waste Monitor the status of waste containers.

Run icon Enables the user to start a run on the instruments.

Feature Description

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2. Click the Protocols tab. The Select Slide Labels view appears.

Figure 8. Create Slide Label

3. Select the label template and protocols.

4. Click the Add button. The selected protocols appear in the Label(s) to Print list. To remove a protocol from

the list, select it, and then click the Remove button.

5. Click the Close/Print button. The Ventana Slide Labeling System view opens.

Figure 9. Enter Slide Label Text

Option What To Do

Label Type Click instrument type.

Select Template The default label template is displayed. If you want to use a different

template, click the list box arrow and select another label template.

Protocol List For each label you want to print, click a protocol. To select multiple

protocols, use CTRL click.

Copies Enter the number of copies to print for the selected protocol.

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6. Type the required fields from your template, and other text you want to appear on the label, and then click

the Print button. The next label moves to the top of the list. Continue entering text and printing each label

until the list is empty.

IMPORTANT: If you modify a protocol, you must also update the label that you print in the SLS. Before

you apply a label to a slide, check that the label includes the correct protocol.

Create a Batch of Slide Labels

You can create a list of labels called a panel and store it in the computer. You can recall the panel later to print

the labels.

1. At the Home View, click the Create Label button. The SLS opens.

2. Click the Protocols button. The Select Slide Labels view appears.

3. Select the label template and protocols for the batch.

4. Click the Save as Panel button. The Enter Name for this Panel dialog box appears. Type a name for the

batch, and then click the Save button.

5. To print the labels, click the Close/Print button. To exit the Select Slide Labels options without printing,

click the Clear button, and then click Close/Print.

Print a Batch of Slide Labels

1. At the Home View, click the Create Label button. The SLS opens.

Figure 10. Create Label Button

Option What To Do

Label Type Click instrument type.

Select Template The default label template is displayed. If you want to use a different

template, click the list box arrow and select another template.

Protocol List Select the protocol you want to use for the batch.

Copies Enter the number of copies to print for the selected protocol.

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2. Click the Protocols button. The Select Slide Labels view appears.

3. Click the Panels tab.

4. Select the name of the batch you want to print, and then click the Add button.

5. To print the labels, click the Close/Print button. The SLS opens.

6. Type the required fields from your template, and other text you want to appear on the label, and then click

the Print button. The next label moves to the top of the list. Depending on your template settings, you can

continue entering text and printing each label until the list is empty.

NOTE: If you selected slide labels to print and then exited SLS without printing them, the labels will

remain selected until you print, remove, or clear them, or exit the VSS. If you click the Cancel or Close

button and leave SLS, the labels will still be selected when you return to SLS.

Remove a Label from the Print List

If you don’t want to print a label, you can remove it from the print list.

1. At the Home View, click the Create Label button, and then click the Protocols button in the SLS.

2. In the Labels to Print list, click the label, and then click the Remove button.

Cancel Slide Label Printing

1. At the Home View, click the Create Label button, and then click the Protocols button in the SLS.

2. Click the Cancel button to stop printing. The system returns to the SLS options but the labels are still

visible. You can choose any of the following options.

Apply a Slide Label

Option What To Do

Protocols button Click it to return to the Select Slide Label options.

Delete Label button Click it to delete the highlighted label from the list. The system prompts

you to verify that you want to delete the label.

Clear button Click it to remove all labels from the list and cancel printing. The system

prompts you to verify that you want to clear all labels from the list.

Print button Click it to return to the SLS and continue printing slide labels.

Close button Click it to cancel printing.

Figure 11. Apply a Slide Label

1. After the label is printed, tear it off carefully.

2. Push the transparent flap (1) over the label (if using

EBAR labels) to seal the printed side. Apply a clear

overlay if using a Zebra label.

3. Peel the label (2) from the backing (3).

4. Apply the label to the frosted side of the slide.

Make sure there are no air bubbles.

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Print Labels from the Order List

You can print slide labels for the order records in the Order List. Slide labels are printed using the default label

template set up in the SLS.

1. Click the Orders button in the Global Navigation.

Figure 12. Global Navigation

2. In the Order List, select one or more orders that need labels. To select multiple orders individually, CTRL

click each order. To select a group of orders, SHIFT click the group.

Figure 13. Order List View

NOTE: Before printing a label, make sure the label printer is connected to the computer, is turned on,

and has enough label stock loaded to print the labels.

3. Click the Printer button and select Label from the print options list.

The system prompts you to confirm that you want to print the selected labels. Click the Yes button to print

labels for the selected orders. Click the No button to exit the print option.

Perform a Staining Run

Running Mode

In Running mode, the system processes slides. To start Running mode, you click the Run button in the

Instrument View.

Figure 14. Startup Modes

The instrument has two modes: Stop Run and Run.

The mode the instrument is in determines what you

can do with it. The mode is set from the software

using Startup Mode buttons at the Instrument

View.

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Start the Staining Run

1. Make sure the reagent hood/cover and drawer are closed.

Print Run Reports

You can print a report that lists reagents, protocols, slide data, and system messages for staining runs that ran to

completion or for stopped runs.

1. At the Home View, click the Reports button.

Figure 16. Home View Reports Button

The Reports options appear.

2. At the Reports View, click Print Run Reports, then click the Successful Runs or Stopped Runs tab. Column

headings are shown on the top line of the grid.

Figure 17. Print Run Reports Button

2. At the Instrument View, click the Run mode button. You are

prompted to confirm that you want to begin a staining run.

3. When the pre-run checklist appears, check the appropriate

boxes, ensuring all checkpoints are correct.

4. The system reads the reagent and slide bar codes, calculates

the staining run time, and starts the run. During the run, the

Instrument Bar shows the countdown to run completion.

Figure 15. Run Time

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• The Run Number, Instrument Name, Operator, Run Start Time, Slide Position, Protocol Name, and

Protocol Number columns are included in all reports.

• The Accession ID, Case ID, and other slide data columns can be added or removed.

3. To choose columns to add to or remove from the report, click the button at the left of the Run No. column.

In the list box, click to check items to include or uncheck items to remove. When you check an item, it

immediately appears in the grid. When you uncheck an item, it immediately disappears from the grid.

When you leave the Reports View, your selections will be saved so the same columns will appear the next

time you return to Reports View.

4. Click the Include Protocol Steps box under the Successful Runs tab if you want to include protocol steps in

the report. When you click the Stopped Runs tab, the Include Protocol Steps box is automatically checked.

5. In the Slide Data Type to Print list box, select the slide data to appear on the report.

6. In the list of runs, click a run, and then click the Print Report button. To select more than one run, use

CTRL click or SHIFT click.

7. A Print Preview window appears so you can review the report before you print it. Click the Printer button

to print the report. When you are finished, click the Close button.

Figure 18. Completed Run Report

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Work With Slides

Edit Slide Data

NOTE: Once staining has started in VSS, changes are not allowed to the bar code field.

Edit or correct errors in the slide data.

1. At the Home View, click the Reports button.

Figure 19. Reports Button

The Reports options appear.

2. Click Print Run Reports. The Successful Runs tab appears.

Figure 20. Successful Runs Tab

3. In the Successful Runs list, click a staining run, and then click the Edit Slide Data button.

Figure 21. Edit Slide Data

4. In the Edit Slide Data form, the Barcode field is the only field that cannot be edited. Click any other cell,

type in new data, and then click the Save button.

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Manage Slide Orders

About the Order List

The Order List helps you manage slides that are being processed. You can scan the list to see which orders are

ready for processing and print a list of required reagents. You can also sort and filter orders, print a list of

orders, or create a new order and add it to the list.

Order List

To open the Order List, click the Orders icon in the Global Navigation.

Figure 22. Order List Features

Orders Sent from an LIS

Feature Description

1 View Use Layout and Group by options to view and organize orders.

2 Reset button Reset list back to default settings.

3 Filter Create a custom filter to sort orders.

4 Quick Find by Value Find an order.

5 Actions Left to right: New Order, Maintenance, and Print.

6 State Key Colors used to indicate the status of slides in the State column.

7 Orders list Lists slide orders currently in the system.

8 Records Displayed Shows the number of order records displayed in the list.

If your facility is linked to a Laboratory Information

System (LIS), check the Orders icon for pending orders

from the LIS. When new orders arrive, the Orders icon

displays a green circle with a number in it.

Figure 23. Orders Received from LIS

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How Orders Are Organized

The Order List organizes slides into order records and displays them in a list. Records appear in the Order List

when a slide label is printed in SLS, a new order record is created, or an order record is sent from the LIS.

The list is sorted in ascending order with the most recent orders at the top. Column headings are defined by the

slide data fields that are set when the host is configured. Some data fields are described below.

Figure 24. Order Data

Column Description

Label Appears black when a label has been printed and gray when a label has

not been printed.

Instrument Shows the instrument identification number.

Position Shows the slide position the slide is in.

State Displays a color-coded status for each slide. Corresponds to the State

Key located above the list.

Protocol Number Lists the protocol number for the order and the slide label.

Protocol Name Lists the protocol name for the order and the slide label.

Patient Name Shows the name of the patient whose tissue is being tested.

Accession ID Lists an identifier used to track an order through the system.

Block ID Lists an identifier used to track a tissue block through the system.

Case ID Lists an identifier used to track a case through the system.

Slide ID Lists an identifier used to track a slide through the system.

Patient ID Used to identify a patient in the system.

Institution Shows the name of the institution performing the test.

Requester Lists the pathologist who requested the test.

Date of Birth Shows the date of birth of the patient.

Gender Shows the patient’s gender.

Date of Surgery Shows the patient’s date of surgery.

Anatomic Site Lists the site where a tissue sample was taken from the patient.

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Organize the Order List

The Order List displays all orders currently in the system. You can move or resize columns, sort column data,

group orders of the same type, or filter out all orders except those you want to see.

Column Options

Use the Column Options List to sort the data in a column.

1. Right-click a column heading. The Column Options list box opens.

2. Select Sort Ascending or Sort Descending. All of the records in the list are sorted by the values in the

heading.

3. To go back to the original order, right-click the column heading again, and then select Clear Sorting.

Move or Resize Columns

To move a column, click the heading and drag it to its new location.

To resize the width of a column, move the column divider between two column headings. When a double-

headed arrow appears, click and drag the column divider.

Sort Column Up or Down

Click a column heading to sort the column data in ascending or descending order. The first click sorts the

column data in ascending order. The second click sorts it in descending order. Notice a small gray arrow shows

the sort order: down means descending order and up means ascending order.

To sort multiple columns, click the first column, then SHIFT click each additional column.

Return to Default Settings

To remove any sort or search options applied to the Order List, click the Reset button. The columns return to

the original settings.

Custom Filters

You can create filters to make it easier to locate a specific order or to sort an order set.

Surgical Procedure Lists any surgical procedure associated with the patient’s care.

Consult ID Shows the name of anyone consulted on a case.

Custom 1 and 2 Fields defined by the laboratory manager and unique to each facility.

Date Entered Shows when the order was entered into the system.

Column Description

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The Order List will remember the last custom filter you applied using the Filter Builder. You can then reapply

the filter directly from the Layout menu.

Figure 25. Filter Buttons

1. To open the Filter Builder, click the Filter button (1), and then click the Customize button (2).

2. In the Filter Builder, you can either set up a new filter or open a filter you created and saved earlier. After

you select or create the filter, click the Apply button. Only the records defined in the filter remain in the

Order List.

Figure 26. Filter Builder

3. If you create a new filter click Save As, enter a name for the filter, and click Save.

4. Click the OK button to close the filter.

5. In the Layout menu, select another option, such as Printed Case Slide Orders. The grid changes to display

the new set of records.

6. To re-use the last filter applied, open the Layout menu again and select Custom.

Figure 27. Retrieve a Custom Filter

Order Maintenance

The Order List provides maintenance options so you can delete out of date or incomplete records from the list.

Because each order is a separate record, you need to delete the record and then save the changes. To restore a

record, you can cancel the changes.

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