Tag Archives: PathologyHorizons

Artificial Intelligence and Computational Pathology: Implications for Precision Medicine

With the advent of digital pathology, there is an opportunity to develop computerized image analysis methods to not just detect and diagnose disease from histopathology tissue sections, but to also attempt to predict risk of recurrence, predict disease aggressiveness and long term survival. At the Center for Computational Imaging and Personalized Diagnostics, our team has been developing a suite of image processing and computer vision tools, specifically designed to predict disease progression and response to therapy via the extraction and analysis of image-based “histological biomarkers” derived from digitized tissue biopsy specimens. These tools would serve as an attractive alternative to molecular based assays, which attempt to perform the same predictions.

The fundamental hypotheses underlying our work are that: 1) the genomic expressions detected by molecular assays manifest as unique phenotypic alterations (i.e. histological biomarkers) visible in the tissue; 2) these histological biomarkers contain information necessary to predict disease progression and response to therapy; and 3) sophisticated computer vision algorithms are integral to the successful identification and extraction of these biomarkers. We have developed and applied these prognostic tools in the context of several different disease domains including ER+ breast cancer, prostate cancer, Her2+ breast cancer, ovarian cancer, and more recently medulloblastomas. For the purposes of this talk Dr. Madabhushi will focus on their work in breast, prostate, rectal, oropharyngeal, and lung cancer.

About Dr. Anant Madabhushi

Dr. Madabhushi is the Director of the Center for Computational Imaging and Personalized Diagnostics (CCIPD). He is also the F. Alex Nason Professor II in the Departments of Biomedical Engineering, Pathology, Radiology, Radiation Oncology, Urology, General Medical Sciences, and Electrical Engineering and Computer Science at Case Western Reserve University.

Madabhushi received his Bachelors Degree in Biomedical Engineering from Mumbai University, India in 1998 and his Masters in Biomedical Engineering from the University of Texas, Austin in 2000. In 2004 he obtained his PhD in Bioengineering from the University of Pennsylvania and joined the Department of Biomedical Engineering, Rutgers University as an Assistant Professor in 2005. He was promoted to Associate Professor with Tenure in 2010. In 2012 he accepted the position of Associate Professor at Case Western Reserve University, Department of Biomedical Engineering and is currently directing a center on computational imaging and personalized diagnostics. He was promoted to full professor in 2014.

Dr. Madabhushi has authored over 150 peer-reviewed journal publications  and over 180 conferences papers and delivered over 240 invited talks and lectures both in the US and abroad. He has over 75 patents either issued or pending in the areas of medical image analysis, computer-aided diagnosis, and computer vision.  He has been the recipient of a number of awards for both research as well as teaching, including the Department of Defense New Investigator Award in Lung Cancer (2014), the Coulter Phase 1 and Phase 2 Early Career award (2006, 2008), and the Excellence in Teaching Award (2007-2009), along with a number of technology commercialization awards.  His research work has received grant funding from the National Cancer Institute (NIH), National Science Foundation, the Department of Defense, private foundations, and from Industry. 

Pathology Horizons 2019

Pathology Horizons is an annual and open CPD event organised by Cirdan to discuss what developments lie ahead in Pathology and what we can do to prepare or take advantage of these. Dr. Harewood will be joined by 13 more international industry experts with some of the topics including:

  • FHIR: transforming the pathology business relationship
  • Cancer Immunotherapy Biomarker
  • Digital Pathology
  • Light-sheet Microscopy
  • Machine Learning in Pathology
  • ctDNA testing for cancer

**Given the boutique nature of this conference places are limited, so please book early to guarantee your place.** Find out more about the speakers, agenda and registration here.

Dr. Louise Harewood to Speak on Cancer Genomics at Pathology Horizons 2019

Dr. Louise Harewood is the Scientific Lead for the Genomics division of the Precision Medicine Centre (PMC) in Belfast, Northern Ireland. The PMC is a new clinical laboratory that brings together high-throughput genomics, digital pathology and big data analytics in a fully integrated fashion. The aim of the centre is to accelerate the translation of potentially relevant diagnostic, prognostic and therapeutic findings into clinically actionable information by applying state-of-the-art technology in a clinical laboratory environment.

Louise has a strong genomics background, based largely around structural rearrangement and copy number variation detection, 3D nuclear organisation and genome regulation. Before joining the PMC, she held a position as an independent postdoc in the Innovation lab at the Cancer Research UK Cambridge Institute, a post created for her to enable continuation of a previous postdoc project and to bring in and develop new techniques within the building.

Talk Title: Cancer Genomics: A Precision Medicine Centre Perspective

Genomic abnormalities play a pivotal role in cancer diagnostics and prognostics, as well as helping to guide treatment choices for individual patients. Although genomic techniques to detect single gene mutations have long since been established in the clinical diagnostic workflow, many other actionable or diagnostic abnormalities, such as structural or copy number variants, continue to be detected by other methods (e.g. FISH, array based methods or cytogenetics) with many different tests often being required for a single patient.

Whilst genomic sequencing techniques, such as whole genome sequencing, can provide all of this information, they have historically been hindered by high costs, long turnaround times and a lack of suitable bioinformatic analysis tools. This, however, is rapidly changing:  – per base sequencing costs have dramatically reduced and sequencing has entered the realms of affordability for many clinical labs. Library preparation and sequencing protocols continue to be improved and made more amenable to automation. There are also a host of computational analysis tools now available on the market with others being continually developed.

The time is approaching when large-scale genomic analyses will be able to replace the multiple individual tests that are currently undertaken for clinical diagnostic purposes in many labs. The generated data will not only allow treatment to be more accurately tailored to individual patients, but also provide vital information about cancer subtypes, risk stratification and provide a vast collection of data that can be re-mined as new biomarkers are discovered.

In this talk, Dr. Harewood will discuss some of the approaches that they are investigating within the PMC with the aim of bringing new genomic technologies into the clinical diagnostic field.

Pathology Horizons 2019

Pathology Horizons is an annual and open CPD event organised by Cirdan to discuss what developments lie ahead in Pathology and what we can do to prepare or take advantage of these. Dr. Harewood will be joined by 13 more international industry experts with some of the topics including:

  • FHIR: transforming the pathology business relationship
  • Cancer Immunotherapy Biomarker
  • Digital Pathology
  • Light-sheet Microscopy
  • Machine Learning in Pathology
  • ctDNA testing for cancer

**Given the boutique nature of this conference places are limited, so please book early to guarantee your place.** Find out more about the speakers, agenda and registration here.

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Clinical metagenomics – are we there yet?

The use of metagenomic sequencing is becoming well-known in human microbiome testing. As high-throughput sequencing becomes more readily available and cost is lowering, more medical testing laboratories are considering the clinical use of shotgun metagenomics.

Clinical applications include identification of infectious agents directly from specimens, including when pathogens are not readily detected using conventional diagnostics. The diagnosis of systemic and central nervous system infections are examples of breakthroughs that have been described. In addition to pathogen identification and microbiome analysis, metagenomics can also be used to explore potential antimicrobial resistance. Clinical metagenomics can assist with therapeutic decision-making, as well as infection prevention and control. Understanding the benefits and barriers in the context of the clinical application is necessary to ensure safe clinical practice and determine regulatory compliance.  

In this presentation, Schlebusch will decode and explore the use of metagenomics in clinical practice.

 About  Dr. Schlebusch

 Dr. Schlebusch is an experienced clinical microbiologist recognised for her research, expertise and implementation of innovative technologies for diagnosis of infectious diseases and antimicrobial resistance. She has been the Director of Microbiology at Mater Pathology in Brisbane for the last 7 years. She has recently been appointed as Staff Specialist at Forensic and Scientific Services, Health Support Queensland. Forensic and Scientific Services is Queensland’s reference laboratory for notifiable conditions and routinely performs whole genome sequencing for disease surveillance, disease outbreaks and research.

Pathology Horizons | 8-10th August 2019

Dr. Schlebusch will present on Clinical Metagenomics at the Pathology Horizons conference  in Queenstown, New Zealand. 

The conference is an annual and open CPD event organised by Cirdan to discuss what developments lie ahead in Pathology and what we can do to prepare or take advantage of these. Dr. Schlebusch will be joined by 13 more international industry experts with some of the topics including:

  • FHIR: transforming the pathology business relationship
  • Cancer Immunotherapy Biomarker
  • Digital Pathology
  • Light-sheet Microscopy
  • Machine Learning in Pathology
  • ctDNA testing for cancer

Learn more and register.

**Given the boutique nature of this conference places are limited, so please book early to guarantee your place.**

Opportunities outweigh the challenges of radiology and pathology integration

Dr. W. Dean Wallace is a Professor of Pathology at the UCLA David Geffen School of Medicine in Los Angeles, California.  Dr. Wallace is the Chief of Pulmonary and Renal Pathology Services and is recognized as an expert in the fields of transplant pathology and lung cancer diagnostics.

Dr. Wallace is also the Director of the UCLA Telepathology and Digital Pathology Center and co-led the team that created the innovative, first of its kind, Integrated Diagnostic Report (IDR) that combines multiple radiology and pathology studies into one dynamic reporting platform.  Dr. Wallace has authored several dozen peer-reviewed papers and book chapters and was lead editor of a textbook in the field of transplant pathology.


Short interview with Dr. Dean Wallace, UCLA, USA at the Pathology Horizons 2018 conference. Dr. Wallace discusses his views on what the future holds for radiology and pathology integration along with the challenges that lie ahead in this area.

If you would like to like to watch Dean Wallace’s full talk from Pathology Horizons 2018- please email earmstrong@cirdan.com.

Interested in attending next year’s conference? Find out more and pre-register here.

Pathology Horizons 2019- The Big Reveal!

We are excited to officially announce that Pathology Horizons 2019 will take place in the exquisite Heritage Hotel in Queenstown, New Zealand. This remarkable venue offers both scenery and atmosphere, located only a short distance from the town centre as well as overlooking breathtaking views of Lake Wakatipu. The CPD conference organised by Cirdan focuses on the future of pathology and attracts an international audience of delegates from a mix of clinical, academic, IT and business backgrounds. Year on year, the conference boasts an impressive speaker panel, including some of the best minds in the area of pathology and laboratory medicine.

Why attend?
This unique conference provides the opportunity to learn about new technologies, procedural developments and lines of research that are driving the future of pathology. This learning is done in a relaxed and fun environment, where delegates are able to network freely with both delegates and speakers.

Who should attend?
Pathology Horizons is open to anyone interested in the area of pathology e.g. Pathologists, Laboratory Managers, Laboratory Technicians,  Biomedical Scientists and Pathology IT. Due to the nature of the conference places are limited, so if you would like to attend remember to book early to avoid disappointment.

What next?

Over the course of the next 8 months we will be revealing the speaker line up and their topics, as well as additional details such as the conference activity and dinner.  Watch this space!

If you would like to be notified when Pathology Horizons 2019 registration opens, please click here.

Application and Implementation of AI Driven Screening Processes in Pathology

Dr. Donal O’Shea, Deciphex

Developing deep learning models that account for all variants of abnormality in a given tissue slide can be a challenge requiring extensive and time consuming annotation of thousands of pathology slides by experienced pathologists. The process also needs to effectively account for tissue processing variance and digital pathology scanner selection, which is almost infinite due to the extensive range of interchangeable unit operations available for the pathology lab.

In scenarios where a high percentage of normal content presents, we propose a generalised model for abnormality detection to help identify abnormal content of interest and support the elimination of normal cases from the workflow.  The generalised model as proposed is developed solely from normal cases, requires no annotation of slides as a result and can be rapidly tailored to account for inter-laboratory processing variance.

During his presentation,“Finding Normals: Application and Implementation AI Driven Screen Processes in Pathology”Dr. O’Shea will discuss how such approaches can be leveraged, useful application segments for the technology and how he foresees this capability being embodied in software workflows.

View more on Dr. Donal O’Shea

About Pathology Horizons

Pathology Horizons is taking place from 13-15 September 2018 at the Lough Erne Resort in N.Ireland. It is a unique CPD conference, organised by Cirdan that looks at what lies ahead in pathology. Delegates will learn about new technologies, lines of research and procedural developments that are driving the future of pathology. View Agenda

Please note that given the nature of this boutique style conference that there are only a limited number of places available. If planning on attending booking soon is advisable. Register here

Laboratory Medicine: The Times They Are A Changin’ – Hear more from Dr. Regan at Pathology Horizons

We are looking forward to welcoming  Dr. Irene Regan, Vice President of the Academy of Clinical Scientists and Laboratory Medicine (ACSLM) in Ireland to Pathology Horizons this September.

Dr. Regan will be giving a presentation, entitled “Laboratory Medicine:  The Times They Are a Changin”, which will focus on the key challenges and opportunities of laboratory medicine and address pertinent issues of the day. The 3 I’s concept will be examined; investing in individuals, investing in ideas and investing in infrastructure in order to deliver a modern and up to date laboratory medicine ecosystem of excellence.

A vision for the future will be presented in relation to re-structuring of laboratory based disciplines taking into account the key challenges that face us today and in the future including; laboratory infrastructure, technology trends, global harmonisation of IVDs, health informatics, e-health, connected health, precision medicine, lab in the home and international competition in healthcare. This vision will be presented keeping in mind the need to ensure high quality and reliability of services.

About Pathology Horizons

Pathology Horizons is taking place from 13-15 September 2018 at the Lough Erne Resort in N.Ireland. It is a unique CPD conference, organised by Cirdan that looks at what lies ahead in pathology. Delegates will learn about new technologies, lines of research and procedural developments that are driving the future of pathology. View Agenda

Please note that this conference is open to anyone interested in the area of pathology, however spaces are limited so booking as early as possible  is advisable. Register here

Genome Sequencing as a Diagnostic Aid

There is wide acceptance of the concept of genotype-phenotype correlation in cancers. This concept has been extensively explored in breast carcinogenesis. Early work identified a strong phenotypic signature of breast cancer, which arose in patients with germline BRCA1 mutation. Subsequent data identified four broad intrinsic subtypes of breast cancer, with one being a group of “basal-like” breast cancers, referring to their over-expression of basal cytokeratin markers. Over time, and with transition of intrinsic subtyping to the clinic, the concept of triple-negative breast cancers (i.e., not expressing ER, PR or HER2 by IHC or ISH) evolved as a phenotypic surrogate for “”basal-like” breast cancers. This surrogate was acceptable, given that therapeutic targets available in breast cancer were limited to those directed at the ER/PR pathway and HER2, neither of which were expressed in basal-like breast cancers.

The genomes of several cohorts of triple negative breast cancer have since been analysed. It is clear that they are a heterogeneous group of cancers at the molecular level, with general agreement that some remain true to the basal-like genotype, whilst others have a predominant “immune-activated” or a “mesenchymal” genomic footprint. Still others are nominated “luminal androgen receptor” and are non-basal-like in their molecular profile.

Concomitantly, there has been evolving interest in targeted therapies for TNBC, including targets for basal-like and luminal androgen receptor breast cancers. However, there has been little application of this refined molecular stratification of TNBC in the clinic, possibly due to inaccessibility of genomic analysis for the majority of breast cancers and the fact that the morphological correlates of these TNBC remain under-explored. New technologies, including digital imaging of histology phenotypes, can potentially be recruited to help determine phenotypic subgroups of TNBC relevant to their genotype and therefore their potential targeted therapies. It is possible that these digitally-discovered phenotypes can be applied to stratify TNBC in the routine clinical setting.

Prof. Jane Armes, Clinical Director at NSW Health Pathology in Australia will be discussing further at Pathology Horizons 2018.

About Pathology Horizons

Pathology Horizons is an annual CPD conference that focuses on what lies ahead in pathology. This unique event allows delegates to learn about new technologies, procedural developments and lines of research that are driving the future of Pathology. Unlike other larger pathology conferences, it is a boutique event with only one conference stream. This enables delegates to interact and network with each other as well as with the expert international panel of expert speakers.

Date: 13-15 September 2018

Venue: Lough Erne Resort, N.Ireland

View full agenda
Early Bird ends 31/5/18 – View details on how to register

Dr. Bankhead to speak on how novel open source software platform is revolutionizing digital pathology image analysis

We are delighted to welcome Research Scientist,  Dr. Peter Bankhead to our expert panel of speakers for Pathology Horizons 2018.

Innovation increasingly relies on open tools, standards and software, empowering researchers to test new ideas and make new discoveries.  Reproducibility and standardization in science also crucially depend upon analysis methods being made freely available.

Until recently, digital pathology suffered from the lack of a software platform that would make these things possible.  Faced with a choice between attempting to analyze whole slide images using commercial systems (often prohibitively expensive) or by applying generic open source software (often prohibitively complex), much biomarker analysis in practice continued to be based on visual estimation by pathologists, which is laborious and known to have limited reproducibility.

QuPath was developed to address these issues, and represents the first widely-used, powerful, flexible, extensible and user-friendly open source platform for whole slide image analysis.  Since its release at the end of 2016, QuPath has been downloaded more than 10 000 times and is used worldwide by research groups in both academia and industry.

A central goal of QuPath is to provide the tools for pathologists and image analysts to better work together, advancing the field more rapidly.

During  his presentation at Pathology Horizons, Dr. Bankhead will outline some of the reasons behind QuPath’s success so far, and describe features currently in development that are set to greatly expand its scope and reach for digital pathology and bioimage analysis applications in the near future.

Why attend Pathology Horizons?

The conference is set to be another interesting and extremely informative event with a range of top international speakers demonstrating the power of new technologies, updates on procedural developments and valuable new lines of research – all in a relaxed and open atmosphere! Unlike other larger pathology events, Pathology Horizons is a boutique conference with one conference stream, which allows you to interact and network fully with the delegates and speakers. The conference is also CPD certified and has been awarded with 9 CPD credits by The Royal College of Pathologists.

Some other topics from speakers include: 

  • Artificial intelligence and what it means for healthcare and patholgy
  • Liquid biopsy and what it can do for detecting/treating ovarian cancer
  • Virtual and augmented reality in digital pathology
  • Genome sequencing as a diagnostic aid

View  full Agenda.

Don’t miss out, secure your place today!

Pathology Horizons 2018                                                                                    Lough Erne Resort, N. Ireland                                                                                        13-15th September

Radiology and Pathology Integration – Opportunities Outweigh the Challenges

In recent years, advances in the field of diagnostic medicine have provided enormous benefits to patients with cancer.  However, the increase in complexity of new testing modalities in pathology and radiology has also led to new challenges in gathering all essential information and forming a coherent diagnostic message for a given case.

Opportunities for optimal patient care may be lost, and diagnostic errors might not be prevented, without a formal integration of the various testing modalities in pathology and radiology.  During his presentation at Pathology Horizons 2018, Dr. Wallace will discuss the challenges of pathology and radiology correlation in the current diagnostic paradigm and the numerous opportunities for improved workflows and patient outcomes with an effective diagnostic integration process.

Dr. W. Dean Wallace  is a Professor of Pathology at the UCLA David Geffen School of Medicine in Los Angeles, California. He is the chief of pulmonary and renal pathology services and is recognised as an expert in the fields of transplant pathology and lung cancer diagnostics. Dr. Wallace is also the Director of the UCLA Telepathology and Digital Pathology Centre and co-led the team that created the innovative, first of its kind, Integrated Diagnostic Report (IDR) that combines multiple radiology and pathology studies into one dynamic reporting platform. Dr. Wallace has authored several dozen peer-reviewed papers and book chapters and was lead editor of a textbook in the field of transplant pathology.

Why attend Pathology Horizons?

The conference is set to be another interesting and  informative event with a range of top international speakers demonstrating the power of new technologies, updates on procedural developments and valuable new lines of research – all in a relaxed and open atmosphere! Unlike other larger pathology events, Pathology Horizons is a boutique conference with one conference stream, which allows you to interact and network fully with the delegates and speakers. The conference is also CPD certified and has been awarded with 9 CPD credits by The Royal College of Pathologists.

Some other topics from speakers include: 

  • Artificial intelligence and what it means for healthcare and patholgy
  • Liquid biopsy and what it can do for detecting/treating ovarian cancer
  • Virtual and augmented reality in digital pathology
  • Genome sequencing as a diagnostic aid

Please note places for the conference are limited. If you are planning on attending, booking soon is advisable.  Register here

Pathology Horizons 2018                                                                                    Lough Erne Resort, N. Ireland                                                                                        13-15th September