The Tissue Image Analytics (TIA) Centre at the University of Warwick is excited to announce the continuation of its esteemed seminar series for the 2024/25 academic year. These seminars are a prime opportunity for researchers, students, and professionals to delve into cutting-edge developments in computational pathology and related fields. Held on the 1st and 3rd Mondays of each month from 2 pm to 3 pm, these sessions are a hub for innovative ideas and collaborative discussions. Over the last three years, we have organised 55 seminars, hosting researchers from 42 different institutions from 13 countries and 7 US states, spanning Europe, North America, Australia and Asia.

Highlights from Last Year’s Seminar Series

The past year featured a diverse lineup of distinguished speakers who shared their groundbreaking work. Notable highlights include:

• Dr. Zhui Huang and Dr. Gabrielle Campanella delivered insightful talks on foundation models, exploring their applications and potential in computational pathology. Prof. Hamid Tizhoosh further discussed foundation models and information retrieval. Georg Wölflein offered a comprehensive comparison on many of these models.
• Prof. Inti Zlobec and Daan Geijs visited in person, discussing their pioneering work on studying tumour budding and skin cancer assessment, respectively, providing attendees with the unique opportunity to engage directly.
• Dr. Andrew Song introduced AI-driven methods for efficient patient prognosis using 3D pathology samples, whilst Prof Stefan Feuerriegal and Valentyn MeIynchuk discussed causal machine learning.
• Many, many more fantastic speakers!

Upcoming Seminar Series

We are excited to announce that the upcoming semester promises another stellar roster of speakers. We will kick off the series with a talk by Dr. Ming Y. Lu from Harvard Medical School on the new “PathChat” model (paper: "A Multimodal Generative AI Copilot for Human Pathology") on Monday 14^th October. We will also be visited in person by Dr. Danielle Belgrave from GSK and Jack Breen from the University of Leeds, who will offer insights into their pioneering work, to name a few!

How to Participate

These seminars offer a platform to learn from and interact with some of the leading minds in the field. If you are interested in attending or wish to present your research at a future seminar, please contact Dr. Adam Shephard at adam.shephard@warwick.ac.uk.

Stay updated on seminar details by visiting our website and watch past presentations on our YouTube channelLink opens in a new window. We continuously update our webpage with new information about upcoming seminars, so be sure to check back regularly.

Photo taken prior to Prof Inti Zlobec’s seminar in July.

Wednesday 3^rd July 2024 saw 30+ colleagues interested in Artificial Intelligence and Pathology descend on Warwick University’s TIA Centre to hold a workshop. Delegates from a variety of disciplines, including pathologists and data scientists, attended the workshop, on Campus. The focus of the workshop was to explore the Future Interface of Computing and Pathology. The meeting was lively and interactive and will be the first in a series of workshops that will be hosted by the TIA Centre in furtherance of this subject area. Thank you to all those who participated. If you would like to join in future workshops please contact the TIA Centre at tia@warwick.ac.uk.

Attending the 20th European Congress on Digital Pathology (ECDP) 2024 in Vilnius, Lithuania, was an enriching experience. Over three days, experts and professionals gathered to exchange knowledge, present innovative ideas, and network. Here are some highlights and personal insights from the event.

Day 1: Integrative Pathology and AI Applications

The conference began with a welcome from Arvydas Laurinavičius and Norman Zerbe. Richard Levenson's keynote on transitioning from whole-slide to no-slide imaging was particularly thought-provoking as he suggested innovative way for tissue imaging that did not require convention microscope or whole slide scanner, however, there is still room for improvement in that area. Sessions focused on integrating molecular and spatial pathology with AI. Highlights included Hannah Williams' work on spatial transcriptomics in colorectal cancer and Spyridon Bakas' research on detecting glioblastoma patterns. Naoko Tsuyama’s talk on AI interpretability for pathologists showcased AI's potential as a powerful tool.

Day 2: Sustainability and Interoperability

Discussions on the second day emphasized the importance of sustainable AI in pathology. The "Odd Couple" session highlighted unique partnerships, followed by talks on interoperability challenges. The "Digital Pathology Neighborhood" session offered global perspectives on digital pathology implementation, featuring Riyad El-Khoury and Abdulaziz Alajlan.

Day 3: Advanced AI Techniques

The final day featured poster presentations and a keynote by Faisal Mahmood on multimodal generative AI for pathology. Sessions delved into advanced machine learning techniques, with Milda Poceviciute’s presentation on addressing generalization challenges being particularly noteworthy. The conference concluded with a panel on leveraging European networks for research and patient benefit.

Contributions from Our Lab

Our lab was well-represented, with several members presenting their research:

• Nasir Rajpoot: Interpretable AI for Precision Histopathology (Nasir also chaired the “Virtual Pathology in Education” session and was active in Histofy booth in the industry section).
• Neda Zamanitajeddin (Myself): Benchmarking Domain Generalization Algorithms in Computational Pathology
• Mostafa Jahanifar: Exploring the Clinical Utility of AI in Mitosis Scoring for Breast Cancer
• Adam Shephard: ODYN: An AI-based Pipeline for Predicting Malignant Transformation in Oral Epithelial Dysplasia
• Mark Eastwood: Multi-task GNN Prediction in Breast Cancer using Deep Features and Cellular Composition Statistics
• Kesi Xu: Is Segment Anything Model Generalizable for Histology Images?

Attending and presenting at ECDP 2024 was a remarkable experience for our team, contributing significantly to our research in digital pathology.

Personal Insights

ECDP 2024 was an interesting experience, highlighting the importance of interdisciplinary collaboration and sustainability in digital pathology. The knowledge and connections gained will significantly contribute to my future research and professional development. Thank you, Vilnius, for an unforgettable experience!

I, Zhao Chen, am an Associate Professor with the School of Computer Science and Technology, Donghua University, Shanghai, China and a Visiting Researcher (01/09/2023-31/08/2024) with the Department of Computer Science, the University of Warwick, UK. My interests are in computational analysis for various kinds of images, including pathology, remote sensing and fabric images.

Thanks to Professor Nasir Rajpoot who kindly invited me and always stood by my side, I finally arrived in the UK in September 2023. The academic visit was delayed for almost three years due to the unexpected Covid. Luckily, Nasir, the whole TIA team, the University of Warwick, my home university and China Scholarship Council (CSC) which sponsored this visit did not give up on me. I’m truly feeling obliged to every one of them.

Honestly speaking, when I first came to the main campus of UW, I was a little surprised by its modern style which is unlike the historical ones of Cambridge or Oxford. However, almost immediately, it filled me with a sense of familiarity as most campus of Chinese universities built in the recent decade, including Donghua where I came from, adopt a similar style-grand buildings with large windows. On my first day, Katie Martin welcomed me on the ground floor of the DCS building and walked me through the registration steps. She is very professional, always ready to answer my questions and fix my problems. The TIA team members have also offered me lots of help as well as fun. The chatting, laughing and food sharing in the staff room are sweet memories that will stay with me forever. Especially thanks to Professor David Epstein and his lovely wife Rona, who invited me to their house on New Year’s Eve and gave me an unforgettable night with their beloved friends and guests.

As for the research in the TIA centre, the works produced here are certainly first-class in the area of computational pathology. I really appreciate the opportunities to attend the weekly meetings and participate in the project on PDL1 slide analysis. I’m deeply impressed by the seriousness everyone takes and the patience they have from data collection to paper publication. I’m more overwhelmed by the relaxed working environment here. In Shanghai, it seems that everybody rushes from one project to another to avoid being under-rated or discarded by the system. However, what researchers really need are not intensive assessment, but to be freed of anxiety, given abundant time to deliberate on their proposals and repeatedly test their hypotheses. Looking on the bright side, I’m glad to see that the academic protocols, ideas, techniques and facilities we have in China are not much different from those in England.

With less than two months left, I’m going to carry on finishing my work in the TIA centre while enjoying every minute I have in the UK. Being a great fan of English novels and drama as well the enchanting sceneries presented by them, I have visited many places during the weekends. The vast fields passed by train, the magnificent house in Chatsworth, the cute cottages in Cotswold, the windy cliff by the seaside in Wales, the black-faced sheep and the angry sea birds, and the bluebells in the woods besides the Gilbert campus of UW, all offered me lots of comfort and soothed my mind.

Thanks to all, this year has been wonderful.

Having come from an engineering background, I decided to pursue my postdoctoral experience in computer science, and I loved it. Just after submitting my thesis in Spring 2023, I started a research position at TIA, working with Dr Shan Raza on early detection of oral cancer and in collaboration with University of Sheffield. Reflecting on my first year at TIA, I have got much to say!

Despite being quite an interesting (and imperative) topic, computational pathology requires a solid understanding of both the technical and clinical aspects of the pathology. So, I embarked on a fascinating learning journey that changed the way I perceived medical research. Not only I got day-to-day guidance and encouragement from my line manager, Shan, but the TIA’s atmosphere of camaraderie and helpfulness nurtured both my work experience as well as my confidence in my work and its importance in the grand scheme. You don’t only learn to model cancer growth at TIA, you also learn the soft skills needed to thrive in a research environment.

Another benefit of working with a research centre that thrives on going above and beyond is that excellence becomes a natural endeavour, and ambition is just infectious. During my first year at TIA, I managed to take part in several conferences in the UK and abroad, published a conference paper, participated in a medical registration challenge, and contributed to the centre’s open-source computational pathology project, TIAToolbox. I also co-applied for a grant application with Shan and Sheffield. During each of those projects, I have worked with different members of the TIA centre, learned new skills encompassing software engineering, deep learning, technical writing, verbal and written communication, project management, and of course, team working.

All in all, the TIA is a unique place where talented individuals team up to solve cancer’s most challenging problems, computationally!

We would like to take this opportunity to thank CRUK for funding the Precision Vision Project and Abdullah’s role in this project.

By Adam Shephard (with the help of Chat-GPT)

I recently travelled to Athens for the ISBI 2024 conference. This was also a great opportunity to travel to Greece, and so my wife and I headed out a few days earlier and stayed on a nearby island called Aegina, just a 30 minute ferry from Athens port. Famed for the Temple of Aphaia, pistachios, and hiking trails, we enjoyed what the island had to offer in a relaxing few days before the conference started. This included plenty of Souvlaki, Mythos and even hiking up Mount Ellanio, the highest mountain in the Saronic Gulf. The combination of spectacular views and the sheer volume of grilled meat made us question if we should stay on the island indefinitely.

Upon returning to Athens, the ISBI conference kicked off, lasting for four action-packed days. Several other TIA members also flew out to attend, including Shan, Abdullah, and Arwa, along with Edward also from DCS. Unfortunately, Shan’s start to the conference was less relaxing than my few days on the beaches of Aegina, having lost his checked luggage on the flight to Athens. Over the course of this conference, we saw many interesting talks and poster sessions. The plenary talk on the first day was by Prof Anant Madabhushi, who gave a fascinating talk on “Getting serious about AI in healthcare: retrospective and prospective validation”. We also attended some great tutorials on “Diffusion Models in Medical Imaging”, which we are hoping to disseminate further at an upcoming centre meeting.

The second evening of the conference featured a “treasure hunt” organized by the conference team, taking us to some of the highlights of Athens, including the Temple of the Olympian Zeus, the Roman Agora, the Ancient Agora of Athens, and Hadrian’s Library, all with the majestic Acropolis looming in the background. It was a great way to blend some sightseeing with networking.

On the third day, I gave an oral presentation on tumour-infiltrating lymphocyte (TIL) scoring. I focused on the TIAger team’s submission to the TiGER Challenge for TIL scoring, where I showcased our algorithm’s performance. It was a great opportunity to present our work on a global stage and received a positive response. Our group’s contributions continued with poster presentations by Arwa, Abdullah and Edward on the penultimate day. Their work seemed to be a success, and saw continued interest and discussion throughout the session. We also had the chance to meet people from different research groups we’ve collaborated with before, which was a real pleasure.

Between conference sessions, we took some time to explore Athen’s historic wonders, with visits to the Acropolis and the Parthenon, leaving us both culturally enriched and sunburned. One particularly memorable event was the "symbolic marathon" that Abdullah and I attended, organized by the conference. Hundreds of ISBI attendees gathered at the Panathenaic Stadium, the birthplace of the modern Olympics and the starting point of all Olympic torch relays. Representing the TIA Centre, and Great Britain, we ran ten laps of the stadium. Although it wasn’t meant to be a race, we managed to finish in the top ten, proudly showcasing the TIA Centre. This was certainly one of the highlights of the ISBI conference, and it’s not every day you get to run in the footsteps of Olympians!

The trip home presented its own challenges. A delayed first flight out of Athens, running nearly two hours behind schedule, left us sprinting through Amsterdam airport in a desperate bid to catch our connecting flight to Birmingham. Despite our efforts, our checked luggage opted for an extended stay in Amsterdam. Luckily, we only had to wait a few days for it to be returned!

In summary, the ISBI 2024 conference was not just an academic success but also an adventure. For those considering attending next year, I highly recommend it—but maybe only take hand luggage!

We would like to take this opportunity to thank CRUK for funding the ANTICIPATE Project and Adam’s role in this project.

Contributions from Our Lab

Adam Shephard [Oral Presentation]: An Automated Pipeline for Tumour-Infiltrating Lymphocyte Scoring in Breast Cancer

Abdullah Alsalemi [Poster Presentation]: An Attention Based Pipeline for Identifying Pre-Cancer Lesions in Head and Neck Clinical Images

Arwa AlRubaiaa [Poster Presentation]: Cell Maps Representation for Lung Growth Patterns Classification in Whole Slide Images

The Tissue Image Analytics (TIA) Centre is delighted to extend its congratulations to Dang Vu for winning the 2024 Best Thesis Prize for the Department of Computer Science. Dang is a former PhD student from the TIA Centre and his thesis was entitled “Handcrafted Representations for Whole Slide Images”.

On winning his award Dang has said “Winning this award is a great honour and a wonderful acknowledgment of my research. I'm grateful for the support and guidance I've received from my advisors and colleagues throughout this journey. This recognition inspires me to continue working hard and contributing to the field of computer science and medical research”.

The award for Dang comes on the back of former students from the TIA Centre winning 4 previous Best Science Faculty Thesis awards in previous years :-

2015 - Adnan Khan

2017 - Korsuk Sirinukunwattana

2019 - Talha Qaiser

2021 - Simon Graham

We are excited to announce that PathLAKE has received funding of £13.5 million towards the PathLAKE Centre of Excellence!

Health Secretary Matt Hancock has emphasised the importance of supporting Artificial Intelligence and embracing technology to save lives.

Please see here for further details.

Follow twitter link here

Join us in the exciting 'Beat the Pathologist' Competition to learn exciting ways to annotate and explore digital pathology! Follow the link for more information & registration.

Opening 17/10/20

Closing 16/11/20

There are three categories:

Up to year 6 (primary)/ Y7-Y11 (secondary)/ Y12-Y13 (Sixth Form)

Prizes are awarded to the top three scorers in each category.

Welcome to the competition! This competition has been created for children to experiment and learn exciting ways to annotate.

Please follow the link here for further information.

There are three main levels:

1. Mild
2. Hot
3. Spicy

Congratulations to Shan Raza who has recently had his jointly first-authored paper on the TRACERx lung cancer trial published in Nature Medicine.

Please follow this link for more information.

We were delighted to host the last ECDP Congress at the scenic Warwick Campus.

For more details please follow this link.

We are delighted to announce the award of a Cancer Research UK (CRUK) Early Detection grant in the amount of £406K to Dr Ali Khurram (Sheffield University) and Prof Nasir Rajpoot for research on developing Artificial Intelligence (AI) algorithms to predict malignant transformation of oral epithelial dysplasia.

Please follow this link for more details