Roche uPath RUO User manual

Brand: Roche

Model: uPath RUO

Type: User manual

uPath ER (SP1) image analysis,

Breast Algorithm Guide RUO

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Publication information

Material number 09411046001

reserved.

Trademarks The following trademarks are acknowledged:

VENTANA, BENCHMARK, CONFIRM, ULTRAVIEW, and

UPATH are trademarks of Roche.

Other product names and trademarks are the property of

their respective owners.

Manufacturer address

eLabDoc Electronic user documentation can be downloaded using

the eLabDoc e-service on DiaLog:

dialog.roche.com

For more information, contact your local affiliate or Roche

Service representative.

Template version Software version Revision date Change description

1.0 1.0 June 2021 Initial Algorithm Guide

y Revision history

Ventana Medical Systems, Inc.

1910 E. Innovation Park Drive

Tucson, AZ 85755

USA

+1 520 887 2155

+1 800 227 2155 (USA)

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Table of contents

Intended use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Symbols and abbreviations . . . . . . . . . . . . . . . . . . . . . . 4

About the system limitations. . . . . . . . . . . . . . . . . . . . . 6

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Overview of uPath RUO enterprise software. . . . . 8

Description of the algorithm test principles . . . . . 9

Using the algorithm workflow. . . . . . . . . . . . . . . . . 9

Opening a case. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Drawing whole tumor ROI. . . . . . . . . . . . . . . . . . . . . . . 13

Selecting tumor area . . . . . . . . . . . . . . . . . . . . . . . . 13

Excluding an area from a ROI. . . . . . . . . . . . . . . . . 14

Deleting a ROI. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Image analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Description of color overlays. . . . . . . . . . . . . . . . . . 17

Performing image analysis . . . . . . . . . . . . . . . . . . . 17

Overriding the slide score manually. . . . . . . . . . . . 18

Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Retriggering failed analysis. . . . . . . . . . . . . . . . . . . 19

Understanding areas to exclude from analysis . . 20

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

4 Intended use

Intended use

The uPath ER (SP1) image analysis, Breast RUO algorithm

is an adjunctive computer-assisted tool that identifies ER

negative and positive tumor cell nuclei within a

pathologist annotated viable tumor region in images of

formalin-fixed, paraffin-embedded neoplastic breast

tissue captured on a VENTANA DP 200 slide scanner.

For Research Use Only. Not for use in diagnostic

procedures.

Symbols and abbreviations

Product names Products and name variants for the products mentioned

in this publication.

Symbols used in the publication

Product names Product name variant

uPath ER (SP1) image

analysis, Breast RUO

uPath ER (SP1) algorithm RUO

CONFIRM anti-Estrogen

Receptor (ER) (SP1) Rabbit

Monoclonal Primary Antibody

CONFIRM anti-ER (SP1)

antibody

uPath RUO enterprise

software version 1.1.1

uPath RUO enterprise

software

VENTANA DP 200 slide

scanner

n/a

Benchmark ULTRA instrument n/a

ultraView Universal DAB

Detection Kit

n/a

y Product names

Symbol Explanation

o List item

u Related topics containing further information

Tip. Extra information on correct use or useful

hints.

r Start of a task

I Extra information within a task

f Result of an action within a task.

c Frequency of a task.

n Duration of a task.

d Materials that are required for a task.

j Prerequisites of a task.

u Topic. Used in cross-references to topics.

y Symbols used in the publication

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Symbols and abbreviations 5

Abbreviations The following abbreviations are used.

p Task. Used in cross-references to tasks.

Figure. Used in figure titles and cross-

references to figures.

Table. Used in table titles and cross-references

to tables.

Symbol Explanation

y Symbols used in the publication

Abbreviation Definition

ER Estrogen Reception

FFPE Formalin-fixed, paraffin-embedded

IHC Immunohistochemistry

ROI Region of interest

RUO Research use only

WSA Whole slide analysis

y Abbreviations

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

6 About the system limitations

About the system limitations

When working with uPath ER (SP1) image analysis, Breast

RUO, cited in this document as uPath ER (SP1) algorithm

RUO, be aware of the following limitations.

The uPath ER (SP1) algorithm RUO is designed to work

with the CONFIRM anti-Estrogen Receptor (ER) (SP1)

Rabbit Monoclonal Primary Antibody, cited in this

document as CONFIRM anti-ER (SP1) antibody. The test

results are only as good as the quality and accuracy of

the immunohistochemistry (IHC) slide that is imaged and

the subsequent image that is analyzed.

q The uPath ER (SP1) algorithm RUO has not been

tested, nor its safety and effectiveness validated when

used with a personal computer from home.

You must validate the staining run by examination of the

control slides to verify that the expected results have

been obtained before images from sample slides are

acquired by the uPath RUO enterprise software.

Follow the manufacturer’s recommendations for the

uPath ER (SP1) algorithm RUO, including using all the

positive and negative quality control materials for each

staining run.

Description of the CONFIRM anti-ER (SP1)

antibody

Use the manufacturer’s recommendations for the

CONFIRM anti-ER (SP1) antibody, including all positive

and negative quality control materials for each staining

run. If the control slides are not acceptable, restain the

tissue until acceptable results are obtained. Follow the

interpretation guidelines in the uPath ER (SP1) algorithm

RUO method sheet.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

About the system limitations 7

Considerations for the uPath ER (SP1)

algorithm RUO

The uPath ER (SP1) algorithm RUO is not designed as a

standalone tool and must only be used by a qualified and

trained pathologist in conjunction with histological

examination and proper controls.

• The uPath ER (SP1) algorithm RUO may generate

incorrect scores if the slide images exhibit abnormal

staining or are improperly scanned.

• The uPath ER (SP1) algorithm RUO was validated on

invasive ductal, lobular, mucinous, and micropapillary

carcinomas. Samples covered grades 1 to 3, scores of

0 to 100%, and tissue biopsies and resections.

• The uPath ER (SP1) algorithm RUO is a tool that

identifies ER negative and ER positive tumor cell

nuclei.

• The uPath ER (SP1) Algorithm RUO was trained to

determine stain intensity using a robust and

representative data set derived from pathologist

assessments.

The uPath ER (SP1) algorithm RUO may misinterpret

some non-tumor cells as tumor cells, especially larger

cells. In most cases there are many more tumor cells than

non-tumor in the annotated area, so this type of error

should not significantly impact the count.

The uPath ER (SP1) algorithm RUO may identify

unstained stromal cells and lymphocytes as negative

tumor cells, which may incorrectly decrease the reported

percent ER positivity. This is more common in high

positive cases and cases with a large lymphocyte

infiltrate, such as medullary carcinomas.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

8 Overview

Overview

In this section

Overview of uPath RUO enterprise software (8)

Description of the algorithm test principles (9)

Using the algorithm workflow (9)

Overview of uPath RUO enterprise software

The uPath RUO enterprise software version 1.1.1, cited in

this document as uPath RUO enterprise software, is an

end-to-end digital pathology software that consists of

image analysis algorithms and a user interface.

The uPath RUO enterprise software with the uPath ER

(SP1) algorithm RUO provides consistent quantitative

assessment of neoplastic breast tissue.

Multiple functions are available for ease of use while

handling a case:

• Viewing of ROIs at various magnifications.

• Adding annotations to cases.

• Taking tissue section measurements.

• Performing image analysis.

• Generating reports.

uPath ER (SP1) algorithm RUO scoring The uPath RUO enterprise software with the uPath ER

(SP1) algorithm RUO assists in the quantitative

assessment of ER protein expression in IHC stained

histologic sections from FFPE neoplastic breast tissue.

The CONFIRM anti-ER (SP1) antibody counts the total

number of target tumor cell nuclei and stratifies them by

whether they are stained or unstained. Stained cells are

also stratified by stain intensity (weak, medium, or

strong). The uPath ER (SP1) algorithm RUO then divides

the number of ER positive tumor cell nuclei by the total

number of tumor cell nuclei to generate the percent ER

positivity.

The uPath ER (SP1) algorithm RUO reports the percent ER

positivity for each ROI and an aggregate score for all

selected ROIs on that slide. You may either accept the

scores provided by the algorithm, or manually override

them.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Overview 9

uPath ER (SP1) algorithm RUO intensity Stained tumor cells are stratified by stain intensity and

categorized as weak, medium, or strong intensity. The

output parameter is displayed as “Weak/Medium/Strong

Intensity Cell Count” in the ROI and Slide Score Panels

within uPath. The reported numbers are cell counts that

are normalized to 100, effectively making the reported

value the percentage of stained cells that fall into each

intensity bin. This is a deviation from other cell counts in

the panels, where the cell count is the absolute cell count.

Description of the algorithm test principles

The uPath ER (SP1) algorithm RUO employs deep

learning and image analysis techniques to obtain a

percent ER positivity.

The uPath ER (SP1) algorithm RUO uses probability maps

to score images of tissue stained with the CONFIRM anti-

ER (SP1) antibody.

Steps in image analysis • Split image into tiles for processing by the

convolutional neural network.

• Detect cells across the entire image.

• Classify cell nucleus as tumor or other types.

• Classify tumor cell nucleus as positive or negative.

• Perform color un-mixing on positively classified tumor

cells to quantify nuclear stain intensity.

• Categorize intensity into weak, medium, or strong.

• Calculate the percent ER positivity by dividing the

number of ER positive tumor cell nuclei by the total

number of tumor cell nuclei.

Tumor cell identification and scoring Cell locations and classifications are identified by parsing

probability maps generated by the deep learning network.

The classification with the highest probability determines

whether cell nuclei are classified as tumor positive, tumor

negative, or other cell types. The overlay only identifies

negative and positive tumor cell nuclei.

Using the algorithm workflow

The workflow for the uPath ER (SP1) algorithm RUO

includes the following:

• Staining with the CONFIRM anti-ER (SP1) antibody.

• Scanning with the VENTANA DP 200 slide scanner.

• Scoring with the uPath ER (SP1) algorithm RUO.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

10 Overview

Antibody Staining The CONFIRM anti-ER (SP1) antibody identifies ER

positive tumor cell nuclei in neoplastic breast tissue.

Tissue samples are stained with the ultraView Universal

DAB Detection Kit on a Benchmark ULTRA instrument.

Follow the recommendations provided in the CONFIRM

anti-ER (SP1) antibody method sheet for tissue

preparation, staining, and review of controls.

Restain the slides if staining does not meet the guidelines

outlined in the CONFIRM anti-ER (SP1) antibody method

sheet.

Scanning The VENTANA DP 200 slide scanner is an imaging device

used to scan, digitize, compress, store, retrieve, and view

digitized images of slide specimens.

u For more information, refer to the VENTANA DP 200

slide scanner User Guide.

Software The uPath RUO enterprise software is customizable to

meet both site and pathologist needs.

u For more information, refer to the uPath RUO

enterprise software User Guide

d Make sure that the following supplies are ready before

starting this procedure:

m uPath ER (SP1) algorithm RUO

m uPath RUO enterprise software

m VENTANA DP 200 slide scanner

m Neoplastic breast tissue slides stained with the

CONFIRM anti-ER (SP1) antibody on Benchmark

ULTRA instrument with the ultraView Universal DAB

Detection Kit.

r To create and analyze slide images

Use a Benchmark ULTRA instrument using the

ultraView Universal DAB Detection Kit to stain a

neoplastic breast tissue sample with the CONFIRM

anti-ER (SP1) antibody on a glass slide.

Scan the slide with the VENTANA DP 200 slide

scanner in BIF file format at 20X magnification and at

one z-plane.

f The VENTANA DP 200 slide scanner transfers the

slide image to the image management system.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Overview 11

Create a case in the uPath RUO enterprise software

either manually in data management or automatically

through communication with the laboratory

information system.

I The uPath RUO enterprise software triggers WSA,

which automatically analyzes the entire scanned

image, and indicates in the viewer when analysis is

complete.

Use the ROI and Exclusion tools to annotate any viable

tumor region.

Review the results, and then either accept the score or

manually override it.

u Related topics

• Retriggering failed analysis (19)

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

12 Opening a case

Opening a case

Manage slide images for uPath ER (SP1) algorithm RUO

in the CASES screen.

j Make sure the following prerequisites are completed

before starting the procedure.

m You must have the pathologist role or the correct

permissions assigned before you can perform this

task.

r To open a case

In the CASES screen, view the cases assigned to you.

Choose a case by doing one of the following:

• Double-click on the desired case.

• Highlight the case and choose the VIEWER tab.

f The VIEWER screen displays the case with all the

images.

u Related topics

• Selecting tumor area (13)

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Drawing whole tumor ROI 13

Drawing whole tumor ROI

In this section

Selecting tumor area (13)

Excluding an area from a ROI (14)

Deleting a ROI (16)

Selecting tumor area

Each ROI that you create and its analysis status is

displayed in the SLIDE PANEL. If you start to create an

annotation and decide not to continue, you can clear the

selection.

c A slide evaluation or analysis is needed.

j Make sure the following prerequisites are completed

before starting the procedure:

m The VIEWER screen is open.

m You must have the pathologist role or the correct

permissions assigned before you can perform this

task.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

14 Drawing whole tumor ROI

r To select a tumor area

Choose a slide, and then magnify the image.

I The pathologist may view each ROI at various

magnifications and analyze it with the uPath ER

(SP1) algorithm RUO.

f The buttons in the ANNOTATION area of the

Quick Action menu bar become available (change

to bright white font).

Choose the ROI button, and then choose an option

from the tool bar.

f The hand cursor changes to a crosshair cursor.

Move the cursor over the tissue section where you

want to create the ROI, and then choose and drag the

cursor to produce the ROI.

f The ROI is created, and an annotation label above

the ROI displays the ROI name and number.

q All annotation types except a text box are

assigned a name that includes a number, such as

ROI#1, or A#1 for an arrow.

Excluding an area from a ROI

You can draw an area on a slide image to exclude it from

the ROI.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Drawing whole tumor ROI 15

j Make sure the following prerequisites are completed

before starting the procedure.

m The VIEWER screen is open.

m You must have the pathologist role or the correct

permissions assigned before you can perform this

task.

r To exclude an area from a ROI

Choose a slide and then magnify the image.

I All images in the case are displayed. Choose an

image by magnifying it or clicking on it.

f The buttons in the ANNOTATION area of the

Quick Action menu bar are activated.

Choose the ROI on the slide image.

I Any existing text, arrow, measurement, and

exclusions are displayed in the SLIDE PANEL.

f The selected ROI is highlighted in blue in the

SLIDE PANEL.

Choose the Exclusion button, and then choose an

option from the list.

Draw the region to be excluded on the image, and

then choose CONFIRM.

u Related topics

• Understanding areas to exclude from analysis (20)

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

16 Drawing whole tumor ROI

Deleting a ROI

You can change the ROI on a slide image.

j Make sure the following prerequisites are completed

before starting this procedure.

m The VIEWER screen is open.

m You must have the pathologist role or the correct

permissions assigned before you can perform this

task.

r To delete a ROI

Choose on the ROI.

f The ROI annotation label pop-up is displayed.

In the annotation label pop-up or the STATUS PANEL

functions area, choose the icon.

I You can also delete the ROI from the ROI

DETAILS panel.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Image analysis 17

Image analysis

In this section

Description of color overlays (17)

Performing image analysis (17)

Overriding the slide score manually (18)

Description of color overlays

A color overlay displays after ROI Analysis is completed.

The overlay disappears while moving the image. It returns

when the image is no longer selected.

Performing image analysis

The uPath RUO enterprise software allows for the

pathologist to select the ROI for each slide to be analyzed.

j Make sure the following prerequisites are completed

before starting the procedure.

m The VIEWER screen is open.

m You must have the appropriate privileges to perform

this task.

Color Overlay result

Yellow Tumor cell nucleus is positive for ER

Black Tumor cell nucleus is negative for ER

y Color overlay

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

18 Image analysis

r To perform image analysis

Choose the whole tumor ROI by doing one of the

following:

• Choose the center of the ROI to be analyzed.

• Choose the ROI in the SLIDE PANEL.

For each ROI, choose the Image Analysis button

either in the SLIDE PANEL or next to the ROI.

f Results are displayed in the SLIDE PANEL: under

Slide Score and next to the ROIs.

Overriding the slide score manually

The uPath RUO enterprise software allows for the

pathologist to review all cases analyzed and change

scores if necessary.

j Make sure the following prerequisites are completed

before starting this procedure.

m The VIEWER screen is open.

m You must have the pathologist role or the correct

permissions assigned before you can perform this

task.

r To override the slide score manually

Choose a slide for the score override, and then from

the SLIDE PANEL.

f The SLIDE SCORE secondary panel is displayed.

Choose the button in the Slide Score area.

In the Percent Positivity field, enter the score, and then

choose the CONFIRM button to save the score.

• (Optional) Enter comments in the comment field.

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uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

Troubleshooting 19

Troubleshooting

In this section

Retriggering failed analysis (19)

Understanding areas to exclude from analysis (20)

Retriggering failed analysis

If an error occurs while performing WSA, an analysis error

message is displayed beneath the slide image.

c As needed.

j Make sure the following prerequisites are completed

before starting the procedure.

m You must have Administrator privileges to perform

this task.

r To retrigger failed analysis

Navigate to Administrator Settings and choose Job

Queue.

I The administrator settings is only available if you

have administrator privileges.

Choose the Failed tab.

f All slides with failed analyses are displayed.

Choose the slide to be analyzed then choose the Start

Job button.

f Slide moves to the Canceled/Completed tab when

done.

Roche Diagnostics

uPath ER (SP1) RUO algorithm v1.0 · 1020567EN · uPath RUO enterprise software · v1.0

20 Troubleshooting

Understanding areas to exclude from analysis

Follow best practices in selecting ROIs. Exclude areas

from ROIs that are typically avoided when scoring

manually. If you disagree with the score given by the

uPath ER (SP1) algorithm RUO, you have the option to

override it.

Areas to exclude from analysis No overlay With overlay

Necrosis

Exclude area from analysis. It can affect

the slide score.

Tissue folds

Exclude area from analysis. It can affect

the slide score.

Off-target staining

Exclude area from analysis. It can affect

the slide score.

Ink

Exclude area from analysis. It can affect

the slide score.

y Areas to exclude from analysis

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Roche uPath RUO User manual

Roche uPath RUO User manual

Roche uPath RUO User manual

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