Digital Pathology Podcast

Weakly supervised AI for pathology w/ Geert Litjens, RadboudUMC

Have you ever wondered what semi-supervised, weekly, and unsupervised artificial intelligence digital pathology models can do to help pathologists? Can we finally stop annotating??? This episode's guest Geert Litjens - a member of the computational pathology group at Radboud University Medical Center explains how semi-supervised and weekly supervised artificial intelligence-based image analysis can help pathologists do better, more time-efficient, and data-efficient digital pathology. Th...

Never miss a piece of digital pathology knowledge ever again! Digital Pathology Place and Pathology News partnership w/ Jonathon Tunstall

There are a few websites online other than the Digital Pathology Place that talk about different aspects of digital pathology. An important one being Pathology News. Pathology News is an online place bringing together the digital pathology vendors and purchasers. It is meant to be a single community for everyone working in the digital pathology space. A community working together on advancing the digital pathology science.  A unique (and my favorite!) feature of the website, NOT AVAILABL...

BigPicture - the largest whole slide repository for AI model development in pathology. Where do we stand at month 15/72?

Deep learning artificial intelligence has entered the field of digital pathology and is here to stay because it consistently outperforms the classical image analysis methods on pathology slides. The only caveat is that to train good deep learning image analysis models we need a lot of whole slide images. Where do we get them? Is there a central repository that can be used for this purpose? Good news, there is one in the making! There is an ongoing  project to create a very large reposi...

How Indica Labs has been helping researchers understand disease through tissue image analysis for over a decade w/ Kate Lillard, Indica Labs

Digital Pathology for Dermatologists. How Pathology Watch managed to incorporate digital pathology in dermatology practices across the US w/ Dan Lambert, Pathology Watch

Digital pathology is supposed to help pathologists provide better patient care and make their lives easier, but what about other doctors, do they even care? Maybe radiologists? Oncologists? Nope…Dermatologists! They do care! And they are the clients of Pathology Watch – a CLIA lab specializing in dermatopathology, that is currently servicing samples from over 65 dermatology clinics in the USA.  Pathology Watch provides an end-to-end digital pathology solution for dermatologists. From proce...

A simple microscope camera, whole slide scanner and everything in between. The different tiers of digital pathology w/ Mike Miller, I. Miller Microscopes

A common misconception about digital pathology is that it is synonymous with whole slide imaging and has a high price point. This is not the case, as one can enter the digital pathology world and benefit from what it has to offer with a simple microscope camera. If we would like a more sophisticated solution, but don't want to get a whole slide scanner or don't have the use case or business case to justify it, no worries, there is enough to choose from! In this episode, Mike Miller from I.M...

How image analysis and artificial intelligence support digital pathology-enabled precision medicine today and what to expect in the future w/ Michael Grunkin, Visiopharm

This episode is brought to you by Visiopharm.  With the regulatory approvals of whole slide imaging systems, digital pathology became the modality for routine diagnostics. Digitalization of pathology is aiming at increasing precision and productivity in the pathology lab, but the adoption of this field is slower than expected.  One of the causes of the slow adoption is that going digital in a pathology lab means a much bigger investment than just the cost of the whole slide scanners for sl...

From digital microscopy to digital pathology through image analysis. How far have we come in 20 years? w/ Michael Grunkin, Visiopharm

Visiopharm is a company offering image analysis software used on pathology images. The software has been on the market for over 20 years and has evolved through the transition of digital microscopy to digital pathology. Digital microscopy provided static tissue images captured through the microscope camera and only branched out into digital pathology with the wider availability and adoption of whole slide scanners. Image analysis spans digital microscopy and digital pathology, and image anal...

How tissue clearing - based 3D immunofluorescence allows for seeing more biology in the tissue w/ Sharla White, ClearLight Biotechnologies

Even though tissues are tridimensional structures, most tissue research is done on two-dimensional tissue slides. This leaves a tremendous amount of biological information on the table. This episodes' guest - Sharla White, Ph.D., the vice president of research and development at ClearLight Biotechnologies explains how tissue clearing and 3D immunofluorescence can take your tissue research to a whole new level.  With the rise of immuno-oncology, the importance of immune cell interactions wit...

DICOM standard for pathology annotations. Why do we need it? w/ David Clunie, PixelMed Publishing

The Digital Imaging and Communications in Medicine (DICOM) standard for digital medical imaging has been around since the 1980s. First adopted in radiology it is slowly spreading in pathology as well. Now with image analysis being an integral part of medical imaging workflows, the question arose if the annotations made on the images should have a standard format as well? And can the same DICOM format be used? With deep learning taking over the medical image analysis field, the answer is a d...

Digital veterinary cytology and social media teaching w/ Kate Baker, Veterinary Cytology Schoolhouse

In the world of anatomic digital pathology, the mention of digital cytology usually causes thoughts of all the challenges associated with it. We are often not aware that digital pathology and image analysis applications started with digital hematology and cytology (e.g. image analysis-based pap smear evaluation) and that in veterinary medicine digital cytology is a booming discipline.  Today’s episode’s guest, Dr. Kate Baker, is a board-certified veterinary clinical pathologist who has embr...

5 ways to make histopathology image models more robust to domain shift w/ Heather Couture, Pixel Scientia Labs

In this episode, we talk with Heather Couture about how to make deep learning models for tissue image analysis more robust to domain shift. Supervised deep learning has made a strong mark in the histopathology image analysis space, however, this is a data-centric approach. We train the image analysis solution on whole slide images and want them to perform on other whole slide images - images we did not train on. The assumption is that the new images will be similar to the ones we train t...

Smart in Media - the virtual microscopy hub w/ Martin Weihrauch MD, Smart in Media

Advanced computer science expertise with the ability to code and a medical degree with over 20 years of clinical experience is a rare combination. This episode’s guest, Martin Weihrauch MD, the co-founder of Smart in Media incorporates this rare combination.  His digital pathology platform originated when he was asked by a pharmaceutical company to provide some interactive entertainment for the participants of a medical congress, something beyond just coffee, and the only thing really attra...

Why machine learning expertise is needed for digital pathology projects w/ Heather Couture, Pixel Scientia Labs

What do cancer and climate change have in common? Both are very serious problems and in both, machine learning (ML) and artificial intelligence (AI) can be used to support potential solutions. Even though these AI applications may seem very different the ML methods used to support work on both problems are very similar.  Today’s episode’s guest, Heather Couture from Pixel Scientia Labs does exactly that – fights cancer and climate change with AI. She is a computer scientist specializing in ...

AI-powered digital diagnostic tools for medical, veterinary and environmental laboratories. How Techcyte uses AI for digital cytology and smears w/ Ben Cahoon, Techcyte

AI-powered algorithms for digital pathology and tissue image analysis are not new, also digital cytology and hematology already have their share of AI algorithms helping pathologists with faster and more accurate diagnoses. But what about parasitology or microbiology? Techcyte has a tool for that as well.   Today my podcast guest is Ben Cahoon, the CEO of Techcyte, a software start-up that provides AI-powered diagnostic tools for everything smearable: fecal, blood, cytology, and microbiology...

Microscope phone adapter that can bring digital pathology to everyone w/ Cade Wilson, Skoped Micro

This episode contains affiliate links. Learn what that means here Have you ever tried to take a picture through your microscope with your smartphone? If you have, you know how much hassle it is to consistently take good, sharp microscope pictures. So maybe, annoyed with how cumbersome it is and how much time it takes, you have already looked for a microscope phone adapter? I know I have, and the one I got from Amazon quickly ended up in my drawer and never saw the light of day again. The pi...

An easy AI tool for pathology image analysis. How Aiforia empowers pathologists and scientists with supervised deep learning w/ Tuomas Ropponen, Aiforia

How many times did you get annoyed when using non-intuitive digital pathology software? Have you already given up on digital pathology and image analysis or are you still looking for something powerful but easy to use?  Today’s guest, Tuomas Ropponen, the chief technology officer at Aiforia, is talking about the creation of a pathology image analysis platform whose core principles are “easy to use” and “accessible” - Aiforia.  Aiforia stands for artificial intelligence (AI) for image analy...

QuPath - open source quantitative pathology not only for pathologists w/ Pete Bankhead, University of Edinburgh

With more than 170K total downloads and over 700 citations in scientific literature, QuPath is arguably the most popular open-source software for quantitative pathology and bioimage analysis. Today’s podcast guest, Pete Bankhead, the author of QuPath, is taking us behind the scenes of his software creation. Even though Pete is now a senior lecturer in digital pathology at the University of Edinburgh, his digital pathology career actually started by accident. With an undergraduate degree in ...

Immuno-oncology 101 w/ Elfirede Nößner, HelmholzZentrum, Visiopharm advisor

This episode is brought to you by Visiopharm Cancer immunotherapy, aka immuno-oncology, is tapping into the power of our own immune system to fight cancer. There are multiple processes and immune cell populations involved in tumor immunology and digital pathology and whole slide imaging has allowed scientists to leverage the power of tissue image analysis to detect and quantify them. Today’s podcast guest, Prof. Elfriede Noessner will walk us through the complexities of the immune system, ...

How to chose a digital slide scanner w/ Doug Stapleton, Hamamatsu

Are you looking for a whole slide scanner for your digital pathology projects? In this podcast episode Doug Stapleton, the Service Manager of the digital slide scanner division of Hamamatsu, is guiding us through this process.   He is listing 10 questions you need to ask before purchasing a whole slide scanner tailored to your digital pathology needs. Question 1: What is your budget and throughput? Question 2: What is your intended use now and in the future? Brightfield, immunofluorescenc...

How to choose a digital slide scanner w/ Doug Stapleton, Hamamatsu

Are you looking for a whole slide scanner for your digital pathology projects? In this podcast episode Doug Stapleton, the Service Manager of the digital slide scanner division of Hamamatsu, is guiding us through this process.   He is listing 10 questions you need to ask before purchasing a whole slide scanner tailored to your digital pathology needs. Question 1: What is your budget and throughput? Question 2: What is your intended use now and in the future? Brightfield, immunofluorescenc...

Virtual H&E. How Instapath uses optical sectioning microscopy to accelerate pathology diagnosis w/ David Tulman, Instapath

Have you ever wondered if the pathology turn-around time could be faster and came to the conclusion that the only way to achieve that is to skip the tissue sectioning and staining? Now it is possible, with optical scanning microscopy by Instapath.  Today’s guest, David Tulman, is the chief clinical officer of Instapath, a small startup using optical scanning microscopy to image fresh tissue without fixing and staining it.  Working as a clinical trial manager exposed David to different area...

Virtual H&E. How Instapath uses optical sectioning microscopy to accelerate pathology diagnosis w/ David Tulman, Instapath

Have you ever wondered if the pathology turn-around time could be faster and came to the conclusion that the only way to achieve that is to skip the tissue sectioning and staining? Now it is possible, with optical scanning microscopy by Instapath.  Today’s guest, David Tulman, is the chief clinical officer of Instapath, a small startup using optical scanning microscopy to image fresh tissue without fixing and staining it.  Working as a clinical trial manager exposed David to different area...

What to consider when choosing an image analysis solution for phenotyping? (part 3) w/ Regan Baird, Visiopharm

This episode is brought to you by Visiopharm. In this third and last episode of the multiplex mini-series with Regan Baird from Visiopharm we look at the considerations when choosing an image analysis software for phenotyping. The two main points to consider when choosing phenotyping image analysis software are segmentation assistance and data visualization.  Segmentation assistance: Before different markers are attributed to different cells in the tissue and cell phenotypes are determin...

How to make sense of multiplex data with phenotyping? (part 2) w/ Regan Baird, Visiopharm

This episode is brought to you by Visiopharm. Multiplex tissue staining can generate large amounts of data to help identify distinct information about particular cells in tissue.  Immuno-oncology is a field where it is common practice to use multiplexing, in particular for cell phenotyping in tissue. Phenotyping is the ability to classify every individual cell in the tissue based on the biomarker panel used. The panels are designed to identify cells of different lineages as well as cell a...

OracleBio's path to GCP compliant image analysis clinical trail support w/ Lorcan Sherry, OracleBio

Founded in 2011 by this episode’s guest, Lorcan Sherry, along with co-founder John Waller, OracleBio entered the digital pathology market with a unique value proposition – to be a contract research organization for tissue image analysis and help other organizations in their biomarker discovery work.  Fast forward 10 years and they evolved from a small service provider into a Good Clinical Practice (GCP) compliant organization supporting clinical trials, but still within the same paradigm of...

Introduction to multiplex for tissue image analysis (part 1) w/ Regan Baird, Visiopharm

This episode is brought to you by Visiopharm. After experimenting with multidimensional, multimarker, and multicolor single-cell imaging modalities during his postdoc at Beth Israel Deaconess Medical Center in Boston, looking at 2D images of tissue stained just with hematoxylin and eosin (H&E) seemed to him a bit simplistic…and then he was tasked with doing tissue image analysis (IA). When relying just on H&E, IA can be a very challenging task. So, to both simplify it and extract more infor...

Accelerating custom design of AI image analysis algorithms for drug development using transfer learning w/ Sylvain Berlemont, Keen Eye

As a computer scientist, he knew that to make a real impact with image analysis there were only two areas: military and life sciences. Sylvain Berlemont, the founder of Keen Eye chose life sciences and never looked back. He started consulting for the industry during his biomedical image analysis research work in academia and he quickly saw that regardless of the applications, the questions asked and the problems to be solved were very similar. Patterns started to emerge and the next logica...

A new generation of whole slide scanners: faster, smarter, and more flexible w/ Don Van Dyke, Bionovation

Smartphone, smartwatch, smart TV...internet of things (IoT) and artificial intelligence of things (AIoT) is ubiquitous. But did it already make it into any of the digital pathology devices? Oh yes! There is a smart whole slide scanner out there. In this episode, I am talking with Don Van Dyke, the chief business officer of Bionovation Biotech. Bionovation holds a patent to a potentially revolutionary scanning technology powered by AI. Due to the ability of the scanner to predict the 3D a...

Reimbursement for digital pathology in the clinic – how does that work? w/ Esther Abels, Visiopharm

Medical tests and procedures can get reimbursed. The basis of the reimbursement are the Current Procedural Terminology (CPT) codes developed by the American Medical Association (AMA).  But how can such a code be obtained for digital pathology which is so much more complex than a group of tests or procedures that could be reimbursed on a fee-for-service basis? According to Esther Abels, Visiopharm’s Chief Clinical and Regulatory Officer, to align the digital pathology reimbursement with its...

Why and how should pathologists keep up with AI? w/ David Harrison, University of St. Andrews

This episode is brought to you by Visiopharm Artificial Intelligence is starting to cross from pathology research into pathology clinical practice. With several AI-based algorithms approved for clinical use in Europe and many more in the making, it is clear that rather sooner than later it will be an integral part of practicing pathology.   Does everyone practicing pathology have to keep up with this new trend? Those who wish not to and are close to retirement probably not, but everyone el...

Why and how should pathologists keep up with AI? w/ David Harrison, University of St. Andrews

This episode is brought to you by Visiopharm Artificial Intelligence is starting to cross from pathology research into pathology clinical practice. With several AI-based algorithms approved for clinical use in Europe and many more in the making, it is clear that rather sooner than later it will be an integral part of practicing pathology.   Does everyone practicing pathology have to keep up with this new trend? Those who wish not to and are close to retirement probably not, but everyone el...

Virtual Immunohistochemistry. How Owkin uses artificial intelligence to generate IHC stains without antibodies w/ Victor Dillard

If you are working with immunohistochemistry (IHC) you know how challenging it can sometimes be to optimize all the steps in the process to obtain a high-quality stain. It often takes testing different antibodies, antibody concentrations, antigen retrieval methods, and incubation times. What if there was a way to produce an IHC stain virtually, without antibodies or even the need to step into the lab? Today's episode's guest is Victor Dillard, the commercial operation director of Owkin. ...

Why and how is AI taking over the tissue image analysis field? w/ Jeppe Thagaard, Visiopharm

Machine learning is not a new technology, but it started to revolutionize pathology relatively recently. The ideal combination of untapped, abundant pathology data necessary to leverage machine learning and the relevance of pathology applications has drawn scientists to this field and caused an artificial intelligence (AI) explosion.   Within just two years from 2018 to 2020 AI-based tissue image analysis went from “cutting edge technology” to “mainstream”. The deep learning explosion start...

HistoQC, an open-source way to control the quality of pathology images

This episode's guest, Andrew Janowczyk, is a computer scientist who has been active in the field of digital pathology since 2008. Before turning to the field of digital pathology he worked across the globe and across industries.   He was a salmon fisherman in Alaska. In Austria at the United Nations (UN) International Atomic Energy (IAE) Agency, he significantly contributed to the work that won the UN IAEA a Nobel Peace Prize. He taught English in China. He helped build an oil facility in ...

How Aira Matrix supports digital pathology with deep learning on demand w/ Chaith Kondragunta

Today’s guest, Chaith Kondragunta, started working on neural network applications as an engineer back in the days when the computing power to fully utilize them was not available yet. This research field had to wait for the technology to catch up with the theoretical concepts. When this was achieved, Chaith harnessed deep learning for data analytics in the financial sector, but always knew, that to make a real difference it should be implemented in health care and medical sciences. This oppo...

Why and how should digital pathology be implemented into clinical practice? w/ Ralf Huss

Implementing digital pathology into clinical practice is a big endeavor and a decision not taken lightly by pathology laboratories. Today’s guest, Dr. Ralf Huss, the chairman of Visiopharm’s advisory board explains: ·       what the biggest benefits of going digital are ·       how to start  ·       and why pathologists will be forced to accept the digital transformation.  Currently, the two greatest benefits of digital pathology which can be taken advantage of by every pathology practic...

DIY AI-based image analysis for pathology. How DeePathology incorporated respect for pathologists' time into their software w/ Chen Sagiv

I met Chen Sagiv in person in 2019 at the European Congress of Toxicologic Pathology in Cologne, Germany after previously interacting for several months on social media. We stayed in touch ever since and started working on several projects together. Because of her expertise and the great relationship we have developed, she is now my go-to person in the computer vision field. Chen is a mathematician and a computer scientist specialized in computer vision. She is the founder of several tech ...

Remote toxicologic pathology. How Deciphex is accelerating the non-clinical drug development phase w/ Donal O'Shea.

The guest of this episode is Donal O'Shea, the CEO, and founder of Deciphex. He has been active in the area of digital pathology essentially since its beginning. He worked in academia and founded several successful digital pathology start-ups before his current one. Deciphex, in contrast to most digital pathology companies, is focused on non-clinical pathology, and its mission is to facilitate the complete digitization of this space and to contribute to the faster turnaround time of drug de...

Digital pathology in a suitcase. How Grundium's portable whole slide scanning microscope expands the reach of telepathology w/ Mika Kuisma

Often those pathologists and scientists who are thinking of starting their journey with digital pathology are intimidated by the workflow changes and investment they will have to make in order to get started. The cost of the equipment and the challenges related to workflow re-design are often a significant barrier for adoption. Good news, there is an alternative! My guest, Mika Kuisma, the CEO of Grundium, together with his colleagues have been working on a solution since 2015. Mika and hi...

What is validation and how to validate an AI image analysis solution with Tom Westerling-Bui from Aiforia

The tools to develop AI models for biomedical image analysis have recently become accessible also for non-computer scientists. With the accessibility to AI tools, the question arises whether the things we build are good enough? How do we check the model? How do we validate it and be sure that when deployed according to the intended use it will perform adequately and help us make the right decisions based on the correct premises? In this episode, Thomas Westerling-Bui from Aiforia explai...

Pro bono telepathology w/ Jared Block and Gabe Siegel.

Jared organized a fundraiser and Gabe donated to the fundraiser, but he didn't donate money, he donated an augmented reality system - basically, the most expensive piece of equipment Jared was raising money for. This collaboration was born on-line when Jared Block from Carolinas Pathology Group in Charlotte, NC published a post about his fundraiser and Gabe Siegel from Augmentiqs read it and realized it was a match - a great contribution could be made to a place in need where solid collabo...

Pro bono telepathology w/ Jared Block and Gabe Siegel.

Jared organized a fundraiser and Gabe donated to the fundraiser, but he didn't donate money, he donated an augmented reality system - basically, the most expensive piece of equipment Jared was raising money for. This collaboration was born on-line when Jared Block from Carolinas Pathology Group in Charlotte, NC published a post about his fundraiser and Gabe Siegel from Augmentiqs read it and realized it was a match - a great contribution could be made to a place in need where solid collabo...

Digital pathology for microscope lovers. How Augmentiqs approaches digital pathology differently w/ Gabe Siegel.

Due to the coronavirus pandemic, so many pathologists need to work from home today. The microscopes and the slides were packed and brought home. Everyone is now on their own. No more knocking at a colleague's door to consult a diagnosis... But what if pathologists could still collaborate with ease, and consult colleagues from their home offices while reading the slides under the microscope? In real-time. What if at the same time they could also have access to image analysis tools while read...

HistoWiz: fast histology and an image database for mining from Brooklyn NY w/ Ke Cheng

She is a researcher herself and during her research, she experienced the great histopathology pain point first hand: it was too slow! So to help researchers solve this problem she created a company - Histowiz, which not only provides fast histology services but also provides her customers access to a centralized pathology image database that can be used for data mining and to a large network of pathologists providing telepathology services. In this interview Ke Cheng, the CEO of Histowiz te...

PathPresenter a tool to make killer pathology presentations and much more w/ Rajendra Singh, MD

Do you remember a presentation where the presenter had to switch between their powerpoint and a whole slide viewer to show a case and do you remember how annoying that was? Or a presentation where the presenter tried to show the highlights of a case with screenshots embedded in their presentation, but they were not representative at all and you wished you could see the whole slide? Now you don't need to repeat these suboptimal experiences. There is a tool that can do it all - create prese...

Proscia’s tools and vision for modern pathology w/ Nathan Buchbinder.

Do you think your pathology laboratory is modern? If so, you have most probably gone digital. Nowadays modern pathology means digital pathology. However, to fully embrace digital pathology a scanner is not enough. You need the correct tools. Tools to manage your whole slide images in a systematic way and artificial intelligence-based tools enhancing your performance. Proscia is offering both.  Today my guest is Nathan Buchbinder, one of the co-founders and Chief Product Officer of Proscia....

How to get microscopes to where there are no microscopes? The X-wow project w/ Yuchun Ding.

For pathologists and scientists microscope does not seem like a luxury, it is an everyday tool necessary to do their jobs. It is not a cheap tool, but there is no option not to have one, especially if you work in a pathology or microbiology lab. Otherwise, you cannot do your job, you cannot help patients, and every day there are so many cases to diagnose. But what to do, in places, where there are as many cases to diagnose, as many patients who need this diagnosis, but a lot fewer microsco...

Welcome to the Digital Pathology Podcast!

In this very first episode, I want to welcome you to the Digital Pathology Podcast. If you are interested in Digital Pathology and medical and scientific advancements, this is a place for you. Every other week we will be publishing interviews, discussion and journal club-type updates on the newest advancements in the field of digital pathology described in the literature.  Support the Show. Become a Digital Pathology Trailblazer and See you inside the club: Digital Pathology Club Membership