Many pathology laboratories are looking to modernise and update their work methods using the latest technology solutions for improved workflow, collaboration, and ultimately faster turn-around times on opinions and diagnosis.

Digital Pathology solutions from Perfekt combine leading technologies from clinical, pathology and IT providers to provide fast online access to tissue samples for pathologists, researchers and educators anywhere in the globe.  These solutions offer an array of benefits.

Collaboration: online whole slide imaging means that referrals and second opinions can be sought and achieved in seconds or minutes rather than days or weeks.  Travel of pathologists or the samples themselves is virtually eliminated.

Faster diagnosis: Computer aided diagnostics, using advanced mathematical methods, can analyse a number of images rapidly looking for anomalies that will later require human attention.

Storage: Large pathology labs in hospitals store tonnes of glass slides each year. Because of access requirements these would need to be on hand for reference. Perfekt’s digital pathology solutions allow for the glass to be stored in low-cost offsite facilities (if at all) whilst pathologists access the online digital repositories for diagnosis.

Digital Pathology as a technology has been with us for many years. Yet, until now, it hasn’t been adopted for mainstream clinical use. Advances in slide scanning times, pathologist shortages and workflow inefficiencies have meant that digital methods are being adopted in Australia and around the world.

In the past, a 40x slide would require in excess of fives minutes to complete a scan. This has meant that the equipment was not capable of keeping pace with the slide output of busy laboratories. Now, slides can be scanned at the same magnification in under one minute, and this performance leap has opened up the possibilities of almost no impact to total slide processing workflows.

World wide, regulatory bodies are looking favourably at digital methods as a viable progression from light microscopy for pathology diagnosis. Reference studies performed by a small number of leading Australian pathology organisations have seen a statistical correlation between the clinical diagnosis of a slide examined under a microscope vs through a digital system. The technology is proven.

Australia’s vast geographical spread creates unique challenges in providing top-quality healthcare in rural locations. Now, with modest network connectivity, slides can be reviewed with a more comprehensive experience than through a microscope, providing instant care outcomes for patients. 

In order to maintain a reference set and share findings between researchers around the world, digital methods are proving to be highly efficient and flexible. Slides are able to be stored and compared. Useful online features allow side by side comparisons instantly. Reports can be published with snapshots captured quickly from online slides. Configurable workspaces can be tailored to group data that is relevant to project studies. Cases can be imported from previous studies and  anonymised. Collaborators can be added as needed, and access rights can be adapted to reflect the dynamic nature of research. Importantly, all access can be audited to ensure the integrity of research data.

Digital Pathology is an enabler for Histology and Histopathology e-learning, transforming training world wide.  Perfekt’s Digital Pathology solutions allow for educators to conference up to 50 students at a time, located anywhere on the globe, whilst examining tissue samples in the highest resolution for teaching accurate diagnosis.

Any online learning environment is only engaging when being immersed, interactively, with the slide image.  Through the software layer of Perfekt’s Digital Pathology offering, Collibio allows for student interactivity in four key ways:

Annotations: clicking on annotations in the Layers pane will provide informative content about marked areas of the slide, whilst moving within the image to the area of the annotation at the level of zoom in use when the annotation was created. 

Forms: Allowing information to be imparted, and input sought on student opinions or assessments of their views of the slide content.  Collibio provides 8 dialog constructs for form design to capture this input:  whole number, decimal , single line and multi-line text boxes, drop down lists, radio buttons, multi-select check boxes and date entry fields.  All content from forms is sent back to the lecturer for assessment via Collibio’s reporting function.

Conferencing: An instructor can lead students in a virtual classroom, with Skype integration, online chat, pass and take control and follow-along capabilities. Importantly, each student user views an original quality image without pixelisation often seen in other remote viewing systems. 

Attached Files and Documents: At the slide folder or image level within the system an educator may upload a file that is a document or image that can be downloaded and opened by the student and displayed using desktop viewing software.

Many early forays into Digital Pathology were afforded by a grant that allowed for the purchase of a scanner. Too often, a complete business case was never built, and the co-requisite IT infrastructure was not purchased and consequently scanned slide images had insufficient storage allocated for them, and slide images were slow to access or sometimes completely inaccessible due to firewall rules or other IT complexities.

Despite very interesting breakthroughs in storage and related technologies, unfortunately there is no black magic that can deliver TBs of storage for free.  A complete solution needs to factor in the following components, all which Perfekt can provide as part of an implementation:

  • Validation for all use cases – a detailed and documented comparison of glass slides vs WSI within the lab that can stand up to scrutiny if tested.  The use of WSI must be statistically comparable to glass slides in microscopes before being adopted.
  • Redesigning workflow: study, streamline, document, proof. Begins with time/motion study, looking for repetitive or unnecessary slide movements that impact productivity and efficiency.
  • Slide Scanner(s) – quantities to purchase, speeds/capacities, where will they be located
  • Computer servers, racks, UPSs
  • Computer storage systems (eg HCP)
  • Image management software (eg Collibio)
  • Other operating system and software licensing
  • Network bandwidth: assessment and possible upgrade
  • Monitors and cabling
  • Optional: Computer Aided Diagnosis/classification/annotation – software, design, integration
  • LIS integration: following results of time and motion study
  • Training of histo-technologists in slide scanning including quality checking
  • Training of pathologists

To help flesh out the tangible and intangible benefits of such a solution, Perfekt offer a Digital Pathology Benefits Discovery Workshop. This workshop is designed to step through a range of areas in careful detail, looking to ensure that those benefits of a solution are realised and can be part of the investment decision.  The deployment of any new system will see benefits attained that were never considered during the planning stage. In our workshop we help to uncover the full extent of these benefits so that a full solution is justified from the outset.

Outline of our consulting offering: Business Justification Workshop Outline

Perfekt’s Digital Pathology solutions begin with the digital slide scanner from manufacturers including: Aperio, Olympus, 3D Histech, Hamamatsu, Leica, Roche, GE/Omnyx, Leica, Philips, Huron and others. Slide scanning is semi-automated and takes between 30 seconds and six minutes per slide. Images are therefore available in surgery for real-time review.

Perfekt have extensive knowledge of the scanners available in the Australian market and have reviewed products and models and are able to advise as to the most appropriate options for any deployment.

Hamamatsu Nanozoomer XRTo meet the needs for diverse functionality, some digital pathology projects will require scanners with different characteristics, such as for frozen sections, bulk scanning, oil immersion; possibly from different vendors. Integrating these scanners into a single seamless solution is something that Perfekt excel in.

While scanners are provided with basic inbuilt viewing software, Perfekt offer the Collibio software from Pixcelldata which is an advanced and innovative web application for managing digital pathology images and associated data. It is designed to allow pathologists to immediately collaborate using images from proprietary scanner systems, and breaks down barriers for adoption of digital pathology.

Collibio allows users to connect instantly to existing digital image repositories and link to authorised images on the server. The image repositories can be generated from scanners of different scanner vendors and can be in different locations. Images are automatically linked into the system as they are scanned.

Within Collibio, access to the images can be shared with other users, and collaboration can occur between pathologists, researchers and students. This can be controlled by administrators through flexible role-based user access. The integrated image viewer allows rapid review of images residing on different image repositories. Images can be annotated with intuitive tools. A conference between users can be initiated effortlessly allowing synchronised viewing of images by all participants. The participants can indicate features of interest using the mouse pointer, and control of image navigation can be passed between users.

Collibio can also be configured to allow fast and secure publishing of images and associated metadata from one Collibio system to another. This can facilitate easy collaboration between different sites.

Collibio is differentiated amongst other Digital Pathology image viewing and management platforms in the following ways:

  • Browser-based delivery. No client software needs to be installed on user computers or devices. 
  • Fast. Designed to support high speed computer interface protocols to provide an experience equal or better than a microscope when displaying these large image files.
  • Multiple image format support. Connect, convert, view and manage digital slides from any scanner vendor.
  • Scalable, from the perspective of both the underlying storage and the number of concurrent interactive online users. Collibio is designed for the most arduous clinical workloads of thousands of slides per day and over 100 online users.

Pathology is the most information intense area in medicine. Server side computer graphics and intelligent information repositories bring pathology into the digital era of medicine. Information intense areas require an innovative approach to storage due to the large amount of information, and should be managed with some care. The large volume introduces a problem with scale, both economical and operational.

Perfekt’s Digital Pathology solution is deployed with a special storage platform from Hitachi Data Systems called the Hitachi Content Platform (or HCP).  The HCP is much more than a standard file server – it is a content repository.

The repository is designed to act as an information repository: the images, referrals, reports and meta-data are stored in normalised vendor neutral wide spread formats, such as XML and pyramidal TIFF. This means that the information itself is not coupled to any specific application or database, everything stored in the HCP is pure information. Clean and organised information makes it easy to comply with legal and regulatory demands, such as HIPAA, CE, FDA and local regional regulations. There is support for both technical and clinical information lifecycle management (ILM) within HCP.

The HCP is a highly-scalable storage platform with options to 80PB.  Importantly its architecture is self-protecting such that it will never need backing up. When a clinical lab might be adding 4TB of slide images each day, you need to think differently about how this data is stored and managed.

To this end, Perfekt see that the breakthrough storage paradigm enabled by Erasure Coding for data protection of large data sets is key for Digital Pathology deployments.  This white paper covers Erasure Coding and its applicability to Digital Pathology in more detail: Erase Coding in Digital Pathology paper

Many pathologists used to a high quality microscope will prefer a top quality digital viewing monitor. There is no specific pathology viewing standard for monitors, and the choice of monitor is very much a personal preference.  However, many of the benefits of professional colour photography monitors apply equally to Digital Pathology.  These are:

More functional Chip Processing Technology, for example a 16bit chip will mean that more tones are available in the monitor providing more detail on the screen particularly in the dark areas and brightest areas.

Wide colour gamut providing more detail in the bright areas such as oxygenated blood.

Digital Uniformity ensuring that the screen colour and brightness is perfectly even over the entire display, to avoid the question of whether the image is better (or more correct) when placed on the left of the screen or the right. This is a technically challenging engineering issue.

Stable colour, ensuring that once set up, it will maintain the same colour conditions for years to come. Regular monitors can have colour drift, which has a detrimental impact when doing colour and detailed critical work. Monitors with a built-in sensor mean the pathologist would not have to think about calibration after the initial set-up (it will auto calibrate on a schedule). 

Monitors designed with these features can provide the pathologist with a high level of confidence knowing they are looking at images that are being displayed in line with an international standard; the same as DICOM 14 for Radiology or the international Photography standard.

When it comes to interacting with a digital image, a standard wheel mouse will provide a richly functional and productive interface for most pathologist users. Work is being undertaken to sample a range of more sophisticated interface devices which more closely simulate the experience of a microscope. 3D CAD (computer aided design) mouse devices are seen as providing another level of functionality.

Traditional image formats such as JPEG and TIFF are limited in the size of the image they can store. As such, they are not suitable for Whole Slide Images, which could be in excess of 10GB for a 100x scan. In an effort to overcome this,  a number of proprietary scanner formats have been developed (e.g. 3DHISTECH .mrxs, Aperio .svs, Roche .bif, Hamamatsu .ndpi, Leica .scn, Olympus .vsi). Each scanner prefers to write content in these formats. 

BigTIFF is the only open viable format.  Collibio uses BigTIFF for normalised images, with the ability to support multiple image scans in one file. Each image scan is composed of multiple JPEG compressed tiles, for their openness, scalability, and speed of data access. Collibio’s developer, Pixcelldata, is committed to openness and full disclosure of the format in use to allow the image to be used in perpetuity.

The question is often raised about DICOM in pathology. This is a patent-protected format that originated from Radiology. Draft DICOM supplement 145 is in place and is designed for pathology images but currently no scanners write output in this format. The format is not neutral and open. The industry is turning against what could be a good standard because of this competitive behaviour.

Come back to this page soon to view our new white paper on Digital Pathology solution implementation. Due late July 2015.


RCPAQAP, who provide external quality assurance for pathology laboratories in Australasia, have chosen Pixcelldata’s Collibio suite as provided by Perfekt for whole slide image visualisation including for ingest, display and management of images hosted for external clients.

RCPAQAP Collibio Press Release

Connecting Spaces

Perfekt played an instrumental role in running a proof of concept of the ConnectingSpaces environment over a five month period in our Melbourne data centre. This allowed ConnectingSpaces personnel to test the Collibio software on our Hitachi Content Platform system.  The decision to proceed with the implementation was based on a sound result for ConnectingSpaces.

Read about the ConnectingSpaces Digital Pathology solution using the solutions from Pixcelldata and Hitachi Data Systems.  Click Here.

University of Western Australia – Meyers Histology Atlas

Perfekt support Professor Geoff Meyer providing hosted whole slide images that sit within this valuable histology learning resource. Images are displayed via Collibio hosted in Perfekt’s Melbourne data centre running from an HCP storage repository. Review the video at:


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