Data and Sessions Management in a Telepathology Platform

Pedro Nunes

, Rui Jesus

, Rui Lebre

1,2 a

and Carlos Costa

Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Portugal

University of A Coru

na, Spain

Keywords:

Whole-Slide Imaging, Collaborative Platform, Digital Pathology, PACS, DICOM, RBAC.

Abstract:

Digital pathology refers to the acquisition, storage, and interpretation of pathological data gathered by scanners

and displayed in a digital environment, using a distributed network system. This paper discusses the challenges

and opportunities of a collaborative platform applied to digital pathology considering the advantages that it

may carry on regarding education and training but also new paradigms of telepathology and telemedicine.

Furthermore, it proposes the implementation of a secure collaborative platform that integrates a web pathology

viewer with personal areas and virtual archives. The described approach introduces a modern collaborative

concept into the digital pathology workﬂow supported by a customized medical imaging infrastructure where

data management is ensured by an innovator DICOM standard multi-repository server. The solution was

designed to serve distinct usage contexts, including telepathology and e-academy.

1 INTRODUCTION

Digital pathology refers to the whole workﬂow since

the scanning of a microscopic image and the associ-

ated metadata, until its distribution and visualization.

It became popular in the last years due to techno-

logical developments and to the increasing trend of

adoption of digital scanners. The digital pathology

scanners produce what is named Whole-Slide Images

(WSI) (Pantanowitz, 2010).

WSI designates the image digitization by scanning

microscopy glass slides (Pantanowitz, 2010; Pan-

tanowitz et al., 2011; Saco et al., 2016). The process

of digitization comprises multiple magniﬁcations and

focal planes, producing high-resolution digital images

that can aggregate several gigabytes of data (Farahani

et al., 2015). Digital pathology is replacing the con-

ventional light microscopy, potentiating new applica-

tions in education, training and diagnosis (Saco et al.,

2016; Triola and Holloway, 2011).

Opposing a traditional pathology environment, the

specimen storage is cheaper as the samples do not

require specialized protection carried out by trained

staff.

A wide variety of advantages emerge from this

modern branch of medical imaging in production and

clinical environments as, for instance, the process of

https://orcid.org/0000-0002-3230-0732

storing and remote viewing, annotation, and report-

ing. Unlike the traditional slides, the whole-slide

images do not deteriorate over time and it is possi-

ble to assure homogeneity of the display quality of

the images (Foster, 2010). Moreover, further pros

come across, for instance, improvements in the diag-

nostic accuracy, integration with hospital information

systems or availability of distributed work processes

as collaborative work and telepathology (Pantanowitz

et al., 2011; Bueno et al., 2016a).

WSI has introduced new methods to teach his-

tology and pathology in the academic ﬁeld that was

not possible until nowadays (Saco et al., 2016; Pan-

tanowitz et al., 2012). The teaching of pathology is

simpliﬁed by the digital trend as the slide can be ac-

cessed simultaneously by as many teachers and stu-

dents as required, and it is only necessary to hold a

computer or a smartphone to operate the image, un-

like the physical specimen which can only be handled

by a handler at a time. Additionally, the availabil-

ity of a slide in the digital format allows the remote

access from anywhere and from any device instantly,

including previous examinations that could be hard to

ﬁnd in the traditional physical archives. Yet, systems

like these demand strong access security since they

can be operated in open networks. Many of the cases

require conﬁdentiality considering the sample private

data related to the patient and the regulations in force

(Abouelmehdi et al., 2018).

Nunes, P., Jesus, R., Lebre, R. and Costa, C.

Data and Sessions Management in a Telepathology Platform.

DOI: 10.5220/0008969904550462

In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 5: HEALTHINF, pages 455-462

ISBN: 978-989-758-398-8; ISSN: 2184-4305

455

Concerning the clinical environment, WSI and

digital pathology make the diagnosis simpler and

faster as the slide can be dynamically viewed, navi-

gated and magniﬁed on screens in a network (Bueno

et al., 2016b). Professional WSI viewers can be in-

tegrated into the hospital databases and be accessed

within the network or made available for research,

remote diagnosis and consultation (second opinions,

among others) (Bueno et al., 2016b; Pantanowitz

et al., 2015). Some authors (Pantanowitz et al.,

2015; Chordia et al., 2016) report a crescent need

for telepathology and digital pathology in the daily

routine practice. In (Chordia et al., 2016), 98% of

the 247 histopathologists interrogated, felt the need

for telepathology and digital pathology. However,

only 34% declared the use of telepathology in medical

practice. These facts may reveal demand for solutions

of telepathology and collaborative platforms not only

for clinical but also for educational purposes.

However, the development of a capable user inter-

face to aid in the adoption of these new technologies

is one of the improvements that can help the teaching

and collaborative diagnosis nowadays. The integra-

tion of new features impossible to include in the tra-

ditional methods became a reality, as the presence of a

thumbnail to allow a fast and immediate panning, the

possibility of annotate regions of interest directly in

the sample and live discussion platform, for instance.

This paper proposes a solution

for the lack of

collaborative platforms suitable for both teaching and

clinical paradigms by deploying a secure architecture

integrated with a digital pathology viewer

. The plat-

form integrates a pure web pathology viewer (screen-

shot in ﬁgure 1) fully compliant with Digital Imaging

and Communications and Medicine (DICOM) stan-

dard and a security layer to restrict and control the ac-

cess to studies (Lebre et al., 2018b), taking advantage

of the Dicoogle open-source project (Valente et al.,

2016) support for WSI storage.

The collaborative viewer supports new features

like an image handling toolbox, shared pointers, and

synchronized actions. In the persistence layer, the

archive server was redesigned to support an innova-

tor multi-repository concept. Data management se-

curity is ensured through the integration of an ac-

counting mechanism speciﬁcally developed to med-

ical imaging environments, allowing the creation of

virtual archives for each user. For instance, it al-

lows the restriction of access to only particular studies

within a group domain. The mechanism allows the

centralization of the storage, creating different per-

missions of access to different institution resources.

Demo Video: https://youtu.be/Mmsb25edcOo

Demo: http://demo.dicoogle.com/pathobox

2 BACKGROUND

2.1 PACS-DICOM Universe

Implementations of Picture Archiving and Communi-

cation Systems (PACS) have risen with the move to-

wards digital radiology (Beckwith, 2016). A PACS

is a set of distinct hardware and software technolo-

gies comprising medical image and data acquisition

equipment, storage equipment, and display worksta-

tion, all of which are integrated by digital networks.

PACS relies on DICOM. DICOM is one of the most

popular standards in the medical imaging ﬁeld (Silva

et al., 2019). DICOM provides a guide to support

interoperability between multiple vendor equipment

and systems (Bidgood et al., 1997).

In the early time of the launching of DICOM, the

propose was to create a standard format for storing

and handling of radiology images (Godinho et al.,

2017). Notwithstanding, other modalities were in-

troduced, such as nuclear medicine or Breast to-

mosynthesis (Beckwith, 2016) and, more recently,

microscopy, as a result of the rapid spread and adop-

tion of the standard. Later on, the publication of

the supplement 145, addressing digital pathology,

boosted the development of the automated whole-

slide scanners (Bueno et al., 2016a).

DICOM standard is being continuously updated

by the addition of new extensions with the goal of

keeping it up-to-date regarding the needs. However,

unlike the traditional patient-centric DICOM infor-

mation model, WSI are considered specimen centric

as the specimen is the most relevant object (Daniel

et al., 2009; Daniel et al., 2011a).

NEMA, the organization behind DICOM, intro-

duced adjustments to the standard foreseeing the sup-

port for WSI, taking into account the necessary adap-

tations to hold the high-resolution images. Nowa-

days, the standard integrates the data elements, the

deﬁnition of the workﬂow of the preparation, acquisi-

tion, handling, and storage of WSI (Beckwith, 2016;

Daniel et al., 2011b).

2.2 WSI Visualization

One of the key challenges of the display and visual-

ization of the whole-slide images is the big amount

of pixels produced by the scanners so the information

may have the required quality. With the increase of

the number of pixels, also the ﬁle size increases, mak-

ing the remote display via a web browser of the sam-

ples difﬁcult. Once their size is much greater than the

regular medical images and cannot be displayed lo-

cally due to the amount of memory available in most

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456

Figure 1: Collaborative web pathology framework screenshot.

Columns

Rows

Intermediate levels

Thumbnail

Base image

Figure 2: DICOM supplement 145 proposes storing Whole-

Slide Images in tiles from a multi resolution hierarchy in

multi-frame object. Adapted from (Daniel et al., 2011a).

computers (Goode et al., 2013). Nowadays, as a result

of the presented challenges, navigation in the digital

slide is performed using a pan and zoom approach.

The solution comprises a pyramid approach (Figure

2). In this pyramid approach, intermediate levels are

generated until the thumbnail is obtained. Figure 3

shows the workﬂow where pathologists must browse

and select a region of interest in the thumbnail for fur-

ther zoom in to a higher resolution.

Nowadays, solutions like Google Maps or Li-

braries Digital Catalogs (e.g., New York Public Li-

brary, National Library of Australia) adopted this ap-

proach for image and maps handling.

2.3 Related Work

In this scope, solutions that support digital pathology

with a collaborative platform on both commercial ap-

plications and scientiﬁc literature were taken into ac-

count. An in-depth analysis of the retrieved studies

was carried out and allowed us to conclude that no so-

lution, commercial or not, is available publicly, sup-

porting a collaborative viewer of DICOM WSI on a

standard PACS.

However, the literature revised reports works

where collaborative systems where multiple users can

access and work on the same image. Daniel et

al. (Daniel et al., 2011a) that Collaborative Digi-

tal Anatomic Pathology can only be achieved using

medical informatics standards. Some authors (Beck-

with, 2016; Daniel et al., 2011a; Tuominen and Isola,

2010) refer to DICOM supplements 122 and 145 as

the standards focusing the whole-slide imaging han-

dling. They also describe how WSI can be integrated

into standards like DICOM and HL7.

In (Lauro et al., 2013), the authors propose a set

of web-based tools to support the workﬂow of digital

pathology consulting and allow the viewing of WSI

over the web. The authors also state that the digital

pathology segment is dominated by a set of vendors

who have developed their own proprietary format and

viewing solutions. Furthermore, it is reported that

most of WSI vendors provide their own viewing so-

lutions. In the cases where the viewer is available, it

only supports the proprietary formats of each vendor,

Data and Sessions Management in a Telepathology Platform

457

(A) (B) (C)

Figure 3: Example of zooming a Whole-Slide Image in the viewer presented. (A) Thumbnail of the digital slide; (B) Interme-

diate level of zoom; (C) Full zoom level of the image.

in a standalone usage.

Chandrakanth et al. (Bernard et al., 2014) presents

guidelines and problems related to the reason why

telepathology for primary diagnosis has not yet be-

come current practice. In the same paper, the au-

thors reveal iPath (Brauchli and Oberholzer, 2005),

a Web-based telepathology platform that permits the

online presentation and discussion of cases within

user groups.

ıaz et al. propose in (D

ıaz et al., 2018) a

web-based telepathology framework for collaborative

work of pathologists. However, this platform does not

comply with the DICOM standard neither addresses

the academic scenarios.

Moreover, the research came across with similar

platforms in the area of radiology (Zhang et al., 2000).

Bankhead et al. (Bankhead et al., 2017) propose an

extensible open-source software for digital imaging

named QuPath, powering users with scripting tools.

However, it does not address the collaborative envi-

ronment and DICOM support.

Carestream

(Snyder et al., 2001; Weiss, 2012) is

a commercial platform built on a consulting basis and

not suitable for collaborative environments. Besides,

Carestream is only applicable to radiology and cardi-

ology modalities.

3 ARCHITECTURE

This section describes the modules that compose the

collaborative platform and the integration with the Di-

coogle PACS repository, intending to provide real-

time collaboration between users. The architecture

was designed to be as ﬂexible as possible, hence why

it is divided into multiple independent modules, mak-

ing it possible to develop and add features to each

module, without affecting the remaining, as well as

completely swap one of the parties while retaining the

https://www.carestream.com/en/gb/medical

functionality.

The system is divided into the following three ma-

jor components: a PACS archive where the case stud-

ies are stored; a web viewer that fetches the slides

from the case studies in the archive; the collabora-

tive platform that informs the viewer about the ses-

sion details and their participants and where the user

can manage their sessions. These interactions are

depicted in Figure 4. The PACS archive and the

Viewer had already been developed in a previous

work (Godinho et al., 2017), however, it was neces-

sary to redesign those elements and implement new

mechanisms to support real-time collaboration be-

tween users.

TogetherJS

is an open-source technology that

provides real-time collaboration features. It is used

by the web viewer to manage the sessions, handling

the synchronization of events across all the participat-

ing users.

The collaborative platform is agnostic to the web

viewer, due to an abstraction layer deﬁned between

the two components that facilitate the use of different

viewers with minimal adaptation efforts. This is pos-

sible because the actions of multiple users throughout

a session can be made abstract, i.e., independent from

the source (viewer) they came from.

3.1 Management of Sessions

A working session is a collaborative session created

over an image from the PACS repository. The col-

laborative platform is responsible for the creation of

these sessions and the management of its participating

users and their permissions. A session is composed by

its creator, a list of users and their respective permis-

sions, the PACS archive image, the list of events that

happened in that session and additional information

to tell the web viewer how to handle this session.

A session is deﬁned by a unique ID that allows the

sessions to be uniquely identiﬁable across the system.

https://togetherjs.com/

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458

WADO-RS

Collaborative

Platform Server

RBAC

Database

Dicoogle

Users and

Sessions Database

Collaborative Platform

Management Interface

Digital Pathology Viewer

HTTP

Web Socket

Digital

Pathology

Plugin

Figure 4: System general architecture. Dicoogle and its plugins serve the Web Viewer with the WSI. At the same time, the

viewer is connected to the collaborative platform server via WebSockets to retrieve the session details and users’ permissions.

The collaborative platform management interface provides a dashboard to manage all the sessions, users, and groups.

This aspect is crucial since one image can have

multiple sessions associated with it, with each ses-

sion having its own users and events. Furthermore,

one user can create multiple sessions using the same

image.

The creation of sessions was designed to facili-

tate the invitation of other users. Therefore, a unique

web link is generated for every user in a session. The

uniqueness of this weblink is guaranteed by combin-

ing the ID of the session with the ID of the user.

Weblinks allow access to a session without having

to use the platform itself. Only the creator is required

to be logged into the platform since it is still necessary

to deﬁne the conﬁgurations of the session. For further

automation of the system, emails are used as IDs to

identify the users on the platform. By using emails, it

is possible to share the web links of the session auto-

matically, turning the process of the invitation of new

users transparent and agile.

Additionally, by sending the invitation links

through email, it is naturally secured the access to this

link, since only the owner of the email has access to

it.

By having the user IDs on the web link, it is pos-

sible to register the sessions that each of the potential

participants were invited to, so that if a user did not

sions he was asked to is still granted, as long as the

email used to sign in is the same as the one sent with

the invitation.

On the viewer side, since the user will be access-

ing it through the web link and the link contains both

the user ID and the session ID, it is possible to query

the collaborative platform for the details of the session

and the permissions of the user. At the same time, it

can also verify if this user already is connected to the

session.

Since sessions are based on web links, the concur-

rent access control is assured by which link is in use

at the current time, due to notiﬁcations sent from the

viewer to the platform, preventing the same link from

being used simultaneously in another viewer, in the

case if a user shared the unique and non-transferable

link. It is, therefore, possible to keep control of the

number of users in a session, and it is assumed that

their identity is also correct since the unique access

links were sent via email.

On the other hand, it is possible to use a pub-

lic link, which is missing the user ID. This modality

seeks to give the creator permissions to invite users

without the need for an email. A limit can be deﬁned

on the number of people that can access a given ses-

sion through a public link. The generation of this link

is optional.

This way, the creator can invite a speciﬁc group

of people without knowing their emails by creating a

public link, with a possible max limit for its usage,

and manually share it. In this scenario, the invited

users can access the viewer session, but would not be

able to access the managing platform, which requires

their email to be added to the session.

3.2 User Actions and Synchronization

To maintain synchronicity between the users, each

event performed upon the image in the Web Viewer,

such as zooming in or changing the saturation, is

broadcast to the remaining users, using TogetherJS.

Data and Sessions Management in a Telepathology Platform

459

This structure allows the separation between the en-

tity which records the actions of the session and the

entity that replicates the session.

Additionally, the events are stored in a database,

ensuring that users that lose the connection temporar-

ily, or are joining in an ongoing session, retrieve the

missing events, keeping up with the rest of the users.

This also allows users to open a standalone copy of a

session, a replay session, replicating chronologically

the events, in which a user can inspect the actions per-

formed.

Since many users can interact with the image at

the same time, certain events can happen in a differ-

ent order from user to user, leading to inconsistent

states throughout the session. Therefore, an asyn-

chronous system is used in which all the users will

eventually be in the same state. Despite having mul-

tiple sessions states across the different viewers, the

database is keeping only one of those versions, which

ultimately will be the ﬁnal one.

Furthermore, only certain actions, like zooming or

panning the image, create these different states, and

all users are sent to the same state right after one of

these events happen, without conﬂict. I.e., when two

different zooms on the image are executed at the same

time, the users might end up on different zoom lev-

els. If a third zoom is effectuated, all of the users will

end up in the same zoom level, keeping all the session

users synchronized. A study was conducted to eval-

uate the impact on the usability of the viewer with

these inconsistencies. Since a user will only be in an

inconsistent state for a very short time and since the

most crucial actions, like color ﬁlters or annotations,

do not cause an inconsistent state, it was considered

that no delay should be added to the propagation of

the action. So, it was concluded that the user actions

should be responded immediately after the execution,

rather than wait for the server conﬁrmation.

Due to the nature of the working sessions and due

to the dimensions of the whole-slide images, many

zooming or panning type of events are generated,

even though they have minimal if any, visual impact.

Thus, despite all events being broadcast to keep the

synchronization between the users, when storing in

the database, the events are ﬁltered, guaranteeing that

only the events that make a noticeable difference are

stored. This prevents a heavy workﬂow of messages

being sent between the components and improves the

loading time of an ongoing session in the web viewer,

as well as, improves the replay experience, due to the

presence of only relevant information.

3.3 Access Control Mechanism

This article proposes a collaborative platform archi-

tecture that supports multiple users with associated

resources, including personal data archives with sen-

sitive information. General Data Protection Regula-

tion (GDPR), applied from May 2018, deﬁnes spe-

ciﬁc guidelines in healthcare and the use of best prac-

tices to minimize the risk of a security breach (art.

32). It requires that personal data needs to be pro-

tected against illegitimate processing, accidental loss,

destruction or damage. Following this regulatory

obligation, the platform was provided with resources

ownership mechanisms that protect resources from

unauthorized access. Those resources may be image

objects, management or organizational services.

As a result, the collaborative system is obligated

to work with a multi-archive paradigm that must be

supported at the persistence layer, i.e., at the stan-

dard medical imaging repository without interfering

with regular DICOM workﬂows. In practice, it is re-

quested an accounting mechanism that must be capa-

ble of associate the repository resources permissions,

and delegation of rights, to third entities. The solu-

tion adopted is based on the Lebre et al. (Lebre et al.,

2018a) RBAC (Role-Based Access Control) mecha-

nism for standard DICOM archives.

The solution provides ownership concept and ac-

cess control over medical imaging resources, allow-

ing to deploy different permissions to multiple users

and institutions. It opens doors to the creation of nu-

merous virtual archives with various studies each that

can be shared between users of different realms. For

instance, digital pathology studies can be shared be-

tween distinct institutions and a working session can

be created with a study shared among multiple users

from different institutions.

The proposed access control model is an abstrac-

tion of real-work medical imaging environments. It

allows the management of Organizations, Facilities,

Users, Permissions, Resources, and Permission Shar-

ing. For instance, in the academic context, the organi-

zation shall be the University. Bellow the hierarchic

position of the organization, the Schools are repre-

senting the Facilities. Belonging to the schools, there

are the Students A, B and C, the Professor and the

Resources 1, 2 and 3. At the collaborative layer, the

security mechanism is allowed to create a session for

a limited number of users who have permission to ac-

cess only some of the studies. Assuming that a class is

composed of students from two distinct departments,

where the studies to be analyzed belong to both the

departments, with this accounting mechanism frame-

work, it is possible to share permissions between stu-

HEALTHINF 2020 - 13th International Conference on Health Informatics

460

dents and professors so that everyone can work in a

collaborative workﬂow. Furthermore, the access can,

hypothetically, be restricted to some hours of the day.

For instance, access can be limited to class time only.

4 USE CASES

This section presents the possible use cases of a col-

laborative pathological viewer. It was already shown

the advantages of using a WSI web viewer to work

on digital pathology samples for diagnosis and aca-

demic purposes. By turning such a viewer into a col-

laborative one, where several users can interact and

discuss one sample at the same time, it extends the

viewer’s utility, improving the concept of telepathol-

ogy. There are two main ﬁelds where a collabora-

tive viewer could prove very useful: the educational

ﬁeld and the clinical environment (Pantanowitz et al.,

2011; Saco et al., 2016; Triola and Holloway, 2011;

Bueno et al., 2016a; Patterson et al., 2011).

In the educational ﬁeld, the presented system al-

lows, for instance, the following use cases:

• Create groups per class and teach that class on-

line, with the possibility of enforcing a schedule

to attend;

• Create an exam and analyze each student’s re-

sponses through the replay tool;

• Give an open lecture allowing the public to follow

it through the public link;

• Create study sessions amongst students.

On the other hand, the clinical research environ-

ment is, perhaps, the environment that beneﬁted the

most from the implementation of an accounting sys-

tem. The introduction of such a mechanism allows

the restriction, control, and auditing of the access per-

formed to speciﬁc patient or study data. Among the

multiple use cases in this ﬁeld, there are cited below:

• Ask for a consultation on a case by inviting a fel-

low doctor into a session;

• Create a work session to discuss a medical case

with other doctors;

• Review diagnostics performed on cases through

the replay feature (if the diagnostic was done on a

previously created session).

Both the environments beneﬁt from services like

the session-catch replay that consists in the fast re-

play of all the operations performed until the present

moment. Additionally, a session administrator may

revoke access and terminate the session.

5 CONCLUSIONS

Collaborative work is a fundamental improvement in

the modern medical image environments, addressing

educational and diagnosis purposes.Digital pathology

and telepathology are an emerging modality in the

clinical decision-making laboratories and with the

clinical staff supporting the development of new tools.

(Bellis et al., 2013). This paper describes an archi-

tecture for a real-time collaborative digital pathology

viewer with access control mechanisms integrated.

The proposed system is based on the concept of work-

ing sessions that can record the actions performed by

the users over time. The design was created using

merely web technologies to address interoperability

with multiple platforms. The potential beneﬁts and

gains in using a system like the one presented are jus-

tiﬁed with the clinical and educational points of view

presented in the use cases section.

ACKNOWLEDGEMENTS

This work has received support from the ERDF Euro-

pean Regional Development Fund through the Oper-

ational Programme for Competitiveness and Interna-

tionalization, COMPETE 2020 Programme, and by

National Funds through the FCT, Fundac¸

ao para a

encia e a Tecnologia within the project PTDC/EEI-

ESS/6815/2014.

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