Upath ER (SP1) 1021934EN - 1

uPath ER (SP1) image analysis,
Breast algorithm RUO user guide

Software version 1.1
1021934EN version 1.0
2
Publication information
Publication version Software version Revision date Change description

1.0 1.1 August 2022 Initial algorithm guide for use with uPath enterprise
software v2.1
y Revision history
Material number 09411046001
Copyright © 2022, Ventana Medical Systems, Inc. All rights

reserved.
Trademarks The following trademarks are acknowledged:
VENTANA, BENCHMARK, CONFIRM, NAVIFY,

ULTRAVIEW, and UPATH are trademarks of Roche.
Other product names and trademarks are the property of

their respective owners.
Manufacturer address
Ventana Medical Systems, Inc.

1910 E. Innovation Park Drive
Tucson, AZ 85755
USA
+1 520 887 2155
+1 800 227 2155 (USA)
eLabDoc Electronic user documentation can be downloaded using

the eLabDoc e-service on Roche DiaLog:
https://dialog.roche.com
For more information, contact your local affiliate or Roche

Service representative.
Roche Diagnostics
uPath ER (SP1) RUO algorithm v1.1 · 1021934EN version 1.0 · uPath enterprise software v2.1
3
Table of contents
Intended use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Symbols and abbreviations . . . . . . . . . . . . . . . . . . . . . . 4
About the system limitations. . . . . . . . . . . . . . . . . . . . . 6
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Overview of uPath enterprise software . . . . . . . . . 8
Description of the algorithm test principles . . . . . 9
Using the algorithm workflow. . . . . . . . . . . . . . . . . 10
Opening a case. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Drawing whole tumor ROI. . . . . . . . . . . . . . . . . . . . . . . 13
Selecting tumor area . . . . . . . . . . . . . . . . . . . . . . . . 13
Excluding an area from a ROI . . . . . . . . . . . . . . . . . 14
Deleting a ROI. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
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
4 Intended use
Intended use
The uPath ER (SP1) image analysis, Breast 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.
For Research Use Only. Not for use in diagnostic

procedures.
Symbols and abbreviations

Product names Products names and product name variants for the
products mentioned in this publication.
Product names Product name variant

uPath ER (SP1) image uPath ER (SP1) algorithm
analysis, Breast
CONFIRM anti-Estrogen CONFIRM anti-ER (SP1)
Receptor (ER) (SP1) Rabbit antibody
Monoclonal Primary Antibody
uPath enterprise software n/a
NAVIFY digital pathology n/a
VENTANA DP 200 slide n/a
scanner
VENTANA DP 600 slide n/a
scanner
BenchMark ULTRA n/a
instrument
ultraView Universal DAB n/a
Detection Kit
y Product names
Symbols used in the publication

Symbol Explanation
o List item.
u Related topics containing further information.
Tip. Extra information on correct use or useful
q
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.
y Symbols used in the publication
Roche Diagnostics
Symbols and abbreviations 5
Symbol Explanation
j Prerequisites of a task.
u Topic. Used in cross-references to topics.
p Task. Used in cross-references to tasks.
Figure. Used in figure titles and cross-
w
references to figures.
Table. Used in table titles and cross-references
y
to tables.
y Symbols used in the publication
Abbreviations The following abbreviations are used:
Abbreviation Definition
ER Estrogen Reception
FFPE Formalin-fixed, paraffin-embedded
IHC Immunohistochemistry
IMS Image management system
LIS laboratory information system
PC Personal computer
ROI Region of interest
RUO Research use only
WSA Whole slide analysis
y Abbreviations
Roche Diagnostics
6 About the system limitations
About the system limitations

When working with uPath ER (SP1) image analysis,
Breast, be aware of the limitations.
The uPath ER (SP1) algorithm 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 to
the level of quality and accuracy of the
immunohistochemistry (IHC) slide that is imaged and the
subsequent image that is analyzed.
q The uPath ER (SP1) algorithm has not been tested,

nor its safety and effectiveness validated when installed
and executed on a personal computer (PC) from home.
You must validate the staining run by examining the

control slides and verify that the expected results are
obtained before the uPath enterprise software acquires
the sample slide images.
Follow the manufacturer’s recommendations for the

uPath ER (SP1) algorithm.
Description of the CONFIRM anti-ER (SP1) Use the manufacturer’s recommendations for the
antibody CONFIRM anti-ER (SP1) antibody, including all positive
and negative quality control materials for each staining
run. If the control slides are unacceptable, restain the
tissue until acceptable results are obtained. Follow the
interpretation guidelines in the CONFIRM anti-ER (SP1)
antibody method sheet.
Considerations for the uPath ER (SP1) The uPath ER (SP1) algorithm must only be used by a
algorithm qualified pathologist in conjunction with histological
examination and proper controls:
• If the slide images exhibit abnormal staining or are
improperly scanned, the uPath ER (SP1) algorithm
may generate incorrect scores.
• The uPath ER (SP1) algorithm is validated on ductal,
lobular, mucinous, and micropapillary carcinomas.
Samples covered grades 1–3, scores of 0 to 10% to
100%, and tissue biopsies and resections.
• The uPath ER (SP1) algorithm is a tool that identifies
ER negative and ER positive tumor cell nuclei.
• The uPath ER (SP1) Algorithm is trained to determine
stain intensity using a robust and representative data
set derived from pathologist assessments.
Roche Diagnostics
About the system limitations 7
The uPath ER (SP1) algorithm may misinterpret some

non-tumor cells as tumor cells, especially larger cells.
Usually 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 may identify unstained

stromal cells and lymphocytes as negative tumor cells,
which may incorrectly decrease the reported percent ER
positivity. This misidentification is more common in high
positive cases and cases with a large lymphocyte
infiltrate, such as medullary carcinomas.
Roche Diagnostics
8 Overview
Overview
In this section
Overview of uPath enterprise software (8)
Description of the algorithm test principles (9)
Using the algorithm workflow (10)
Overview of uPath enterprise software

The uPath enterprise software version 2.1, cited in this
document as uPath enterprise software, is a digital
pathology software that consists of image analysis
algorithms and a user interface.
The uPath enterprise software with the uPath ER (SP1)

algorithm 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 scoring The uPath enterprise software with the uPath ER (SP1)
algorithm helps with the quantitative assessment of ER
protein expression in IHC stained histological 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 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 reports the percent ER

positivity for both ROI and an aggregate score for all
selected ROIs on that slide. You may accept the scores
provided by the algorithm or manually override them.
Roche Diagnostics
Overview 9
uPath ER (SP1) algorithm intensity Stain intensity and categorized as weak, medium, or
strong intensity stratifies cell locations and classifications.
The output parameter is displayed as
“Weak/Medium/Strong Intensity Percentage” in the ROI
and Slide Score panels within uPath. The reported
numbers are cell counts that are normalized to 100, which
effectively makes the reported value the percentage of
stained cells that fall into each intensity bin. This
misidentification 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 employs deep learning and
image analysis techniques to obtain a percent ER
positivity.
The uPath ER (SP1) algorithm 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 cell nucleus
types.
• Classify tumor cell nucleus as positive or negative.
• Perform color unmixing 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 Parsing probability maps generated by the deep learning
network identifies cell locations and classifications. 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.
Roche Diagnostics
10 Overview
Using the algorithm workflow

The workflow for the uPath ER (SP1) algorithm includes
the following:
• Staining with the CONFIRM anti-ER (SP1) antibody.
• Scanning with the VENTANA DP 200 slide scanner or
the VENTANA DP 600 slide scanner.
• Scoring with the uPath ER (SP1) algorithm.
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 and VENTANA DP

600 slide scanner are imaging devices 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 or the VENTANA DP 600
slide scanner User Guide.
Software The uPath enterprise software and NAVIFY digital

pathology are customizable to meet both site and
pathologist needs.
u For more information, refer to the uPath enterprise
software User Guide.
j Make sure the following requirements are completed

before starting this procedure:
m You have an active uPath ER (SP1) algorithm license.
m You have a Benchmark ULTRA instrument with the
ultraView Universal DAB Detection Kit.
Roche Diagnostics
Overview 11
r To create and analyze slide images
1 Stain a neoplastic breast tissue slide with the

CONFIRM anti-ER (SP1) antibody.
2 Scan the slide in BIF file format at 20X magnification

and at 1 z-plane.
f The slide image is transferred to the image
management system (IMS).
3 Create a case manually in data management or

automatically through communication with the
laboratory information system (LIS).
I The whole slide analysis (WSA) automatically
analyzes the entire scanned image and indicates in
the viewer when analysis is complete.
4 Use the ROI and Exclusion tools to annotate any viable

tumor region.
5 Review the results, and then accept the score or

manually override it.
u Related topics
• Retriggering failed analysis (19)
Roche Diagnostics
12 Opening a case
Opening a case
Manage slide images for uPath ER (SP1) algorithm in the
CASES screen.
j Make sure the following requirement is completed before

starting the procedure:
m You must have the Pathologist role or custom
permissions in the uPath enterprise software.
r To open a case
1 In the CASES screen, view the cases assigned to you.
2 Choose a case by doing one of the following:

• Double-click 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
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 (15)
Selecting tumor area

Each region of interest (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.

before starting the procedure:
m The VIEWER screen is open.
r To select a tumor area
1 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.
f The buttons in the ANNOTATION area of the
Quick Action menu bar become available (change
to bright white font).
2 Choose the ROI button, and then choose an option

from the tool bar.
f The hand cursor changes to a crosshair cursor.
Roche Diagnostics
14 Drawing whole tumor ROI
3 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 field 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.

r To exclude an area from a ROI
1 Choose a slide and then magnify the image.

I All images in the case are displayed. Choose an
image by magnifying it or clicking it.
f The buttons in the ANNOTATION area of the
Quick Action menu bar are activated.
Roche Diagnostics
Drawing whole tumor ROI 15
2 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.
3 Choose the Exclusion button, and then choose an

option from the list.
4 Draw the region to be excluded on the image, and

then choose CONFIRM.
u Related topics
• Understanding areas to exclude from analysis (20)
Deleting a ROI
You can change the ROI on a slide image.

Roche Diagnostics
16 Drawing whole tumor ROI
r To delete a ROI
1 Choose the ROI.

f The ROI annotation label pop-up is displayed.
2 In the annotation label pop-up or the STATUS PANEL

functions area, choose the delete button.
I You can also delete the ROI from the ROI
DETAILS panel.
Roche Diagnostics
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.
Color Overlay result
Yellow Tumor cell nucleus is positive for ER
Black Tumor cell nucleus is negative for ER
y Color overlay
The overlay disappears while moving the image. It returns

when the image is no longer selected.
Performing image analysis

The uPath enterprise software allows for the pathologist
to select the ROI for each slide to be analyzed.

Roche Diagnostics
18 Image analysis
r To perform image analysis
1 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.
2 For each ROI, choose the Image Analysis button 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 enterprise software allows for the pathologist
to review all cases analyzed and change scores if
necessary.

r To override the slide score manually
1 Choose a slide for the score override.
2 From the SLIDE PANEL, choose the button in the

Slide Score section.
f The SLIDE SCORE secondary panel displays.
3 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.
Roche Diagnostics
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 requirement is completed before

starting the procedure:
m You must have custom permissions with administrator
privileges in the uPath enterprise software.
r To retrigger failed analysis
1 Log in to the uPath enterprise software.
2 Navigate to Administrator Settings and choose Job

Queue.
3 Choose the Failed tab.

f All slides with failed analyses are displayed.
4 Choose the slide to be analyzed then choose the Start

Job button.
f Slide moves to the Canceled/Completed tab when
done.
Roche Diagnostics
20 Troubleshooting
Understanding areas to exclude from analysis

Exclude areas from ROIs that are typically avoided when
scoring manually. If you disagree with the score given by
the uPath ER (SP1) algorithm, you may override it.
Areas to exclude from analysis No overlay With overlay

Necrosis
Exclude area from analysis. It can affect
the slide score.
.
Tissue folds
the slide score.
Off-target staining or DAB trapping

the slide score.
Ink
the slide score.
y Areas to exclude from analysis
Roche Diagnostics
Troubleshooting 21
Areas to exclude from analysis No overlay With overlay

Endogenous pigment
the slide score.
Ductal carcinoma in situ or atypical

ductal hyperplasia
the slide score.
Normal epithelium
the slide score.
y Areas to exclude from analysis
Descriptions of lymphocyte infiltrate H&E No overlay With overlay

The 3 corresponding images to the right demonstrate
lymphocyte infiltrate and how the uPath ER (SP1)
algorithm may misidentify cells.
Exclude lymphocyte rich areas from analysis or
manually override score.
y Lymphocytes infiltrate
Roche Diagnostics
22 Troubleshooting
Roche Diagnostics

Upath ER (SP1) 1021934EN - 1

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Upath ER (SP1) 1021934EN - 1

Uploaded by

Copyright:

Available Formats

uPath ER (SP1) image analysis,

Breast algorithm RUO user guide

Publication version Software version Revision date Change description

Material number 09411046001

Copyright © 2022, Ventana Medical Systems, Inc. All rights

Trademarks The following trademarks are acknowledged:

VENTANA, BENCHMARK, CONFIRM, NAVIFY,

Other product names and trademarks are the property of

Ventana Medical Systems, Inc.

eLabDoc Electronic user documentation can be downloaded using

For more information, contact your local affiliate or Roche

For Research Use Only. Not for use in diagnostic

Symbols and abbreviations

Product names Product name variant

Symbols used in the publication

Abbreviations The following abbreviations are used:

About the system limitations

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

q The uPath ER (SP1) algorithm has not been tested,

You must validate the staining run by examining the

Follow the manufacturer’s recommendations for the

The uPath ER (SP1) algorithm may misinterpret some

The uPath ER (SP1) algorithm may identify unstained

Overview of uPath enterprise software

The uPath enterprise software with the uPath ER (SP1)

Multiple functions are available for ease of use while

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

The uPath ER (SP1) algorithm reports the percent ER

Description of the algorithm test principles

The uPath ER (SP1) algorithm uses probability maps to

Using the algorithm workflow

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

Follow the recommendations provided in the CONFIRM

Restain the slides if staining does not meet the guidelines

Scanning The VENTANA DP 200 slide scanner and VENTANA DP

Software The uPath enterprise software and NAVIFY digital

j Make sure the following requirements are completed

r To create and analyze slide images

1 Stain a neoplastic breast tissue slide with the

2 Scan the slide in BIF file format at 20X magnification

3 Create a case manually in data management or

4 Use the ROI and Exclusion tools to annotate any viable

5 Review the results, and then accept the score or

j Make sure the following requirement is completed before

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

2 Choose a case by doing one of the following:

Drawing whole tumor ROI

Selecting tumor area

c A slide evaluation or analysis is needed.

j Make sure the following requirements are completed

r To select a tumor area

1 Choose a slide, and then magnify the image.

2 Choose the ROI button, and then choose an option

3 Move the cursor over the tissue section where you

q All annotation types except a field are assigned a

Excluding an area from a ROI

j Make sure the following requirements are completed

r To exclude an area from a ROI

1 Choose a slide and then magnify the image.

2 Choose the ROI on the slide image.

3 Choose the Exclusion button, and then choose an

4 Draw the region to be excluded on the image, and