BIA seminar series

The primary goal of this seminar series is to provide a dynamic platform for bioimage analysts, enabling the community to stay up to date with the latest developments in the field and foster community interactions. The seminars are designed to cater to intermediate and advanced analysts, focusing on practical, high-level content that extends beyond basic instruction.

Target Audience

The seminars are tailored for bioimage analysts who have intermediate to advanced knowledge in the field. This includes professionals and academics who are currently practising or researching within the domains of bioimage analysis, microscopy, and related life sciences. Themes are designed to cover relevant aspects and latest “news” of bioimage analysis, ensuring a comprehensive learning experience for intermediate to advanced analysts. Each session may feature one or two talks, depending on the complexity of the topic and the expertise of the speakers. 

The seminar series will concentrate on a topic for three sessions in a row. The seminar will usually be in the last week of the month, but to help engagement of the global community we will not have a fixed day and time. 

Planned topics so far include:

• Large Language Models

• Infrastructure for deploying image analysis workflows

• Current and future plans for essential BIA tools

• Best practices to build a bioimaging project starting from a user request: what to include, what to ask, how to deliver it? 

• to be continued.....

Registration

Please register for the seminar series here: BIA seminar series. 

The registration will be used to send you the link to the seminar sessions. You will be registered for all upcoming GloBIAS seminar sessions in the future.

 Fourth Topic

Infrastructure - Best practices to build a bioimaging project starting from a user request 

Please find below the information for the fourth set of GloBIAS seminars starting in July:

Title: Euro-BioImaging: From bioimaging projects to communities 

Aastha Mathur, Head of Image Data Services, Euro-BioImaging ERIC, Heidelberg, Germany

Thursday 24. July, 16:00 CEST

Euro-BioImaging ERIC is the European Research Infrastructure for biological and biomedical imaging, providing open access to the latest imaging technologies, training and image data services. There are 41 Euro-BioImaging Nodes, made up of 247 internationally recognized imaging facilities, that offer a full range of services for both biological and biomedical imaging. Euro-BioImaging also offers its users Image Data Services, including standalone Image Data Analysis services through its Nodes. Additionally, Euro-BioImaging also provides technical and data stewardship support, and coordinates user access and participation in community initiatives and various data-centric EU projects.  In this talk I will share with you our user support data services as well as community engagement activities.  

Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit.

Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden

Wednesday, 27th of August, 2pm CEST 

Life science has become more and more multidisciplinary, combining technologies that require high level of expertise. To effectively combine different methods, scientist nowadays can rely on dedicated support groups. We, 6 bioimage analysts in the SciLifelab Bioimage Informatics Unit (BIIF) - provide such support for bioimage analysis. In 2024, we assisted 44 groups all over Sweden through consultations and the development of tailored image analysis solutions. In parallel, we contributed to 7 courses for training on image analysis. TissUUmaps - software for exploring spatial transcriptomics data co-developed by BIIF, reached 5000 downloads/month, and our YouTube channel had 16.500 views over the year.

In this webinar I will offer insights into the operational aspects of BIIF: what is important when managing these activities? What is important when starting-up a new support project?

The scientific added value of a core-facility dedicated to Bioimage Analysis services.

Jean-Yves Tinevez, Institut Pasteur

Monday, 22nd of September, 4 pm CEST

In the last decade or so, the rise of quantitative approaches in biological imaging has spurred new demands for access to image analysis techniques. Various initiatives, such as NEUBIAS, have played a crucial role in shaping a new position in academic research: the bioimage analysts. These experts bridge the needs of a research project with existing tools and techniques in bioimage analysis, creating bespoke analysis pipelines, adapting, or developing tools to address specific questions in Biology. Bioimage analysis core facilities are currently emerging as dedicated structures that house analysts and provide services to a broad scientific community.

In this talk, I will present the Image Analysis Hub of the Institut Pasteur, a core facility dedicated to services in Bioimage Analysis. Established in early 2018, we were one of the first core facilities dedicated to bioimage analysis. I will outline the services we deliver, what we don't offer, and the reasoning behind these choices. I will discuss our current organizational structure, useful policies we have implemented, and the lessons we've learned in establishing the core.

Additionally, I will introduce some of the tools we have built, such as TrackMate, and explain how their development is aligned with scientific added-value for our users. Finally, I will also discuss our efforts to extend beyond addressing the needs of our local scientific community by building a nationwide, remotely-operating core facility under the auspices of France-Bioimaging.

Third topic

Current and future plans for essential BIA tools  

Please find below the information for the third set of GloBIAS seminars starting in March.

QuPath for bioimage analysis: what’s new & what’s next?

Dr Peter Bankhead, Reader, Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, UK

Wednesday, 26. March 2025 4 - 5 pm CET (3 - 4 pm GMT)

QuPath was first released in 2016 with the goal of providing a user-friendly, open-source software application for whole slide image analysis. Now approaching its 9th birthday, QuPath has become a more powerful and versatile platform that can handle a variety of image types, including highly-multiplexed datasets. This seminar will introduce some of the new features added in the latest QuPath release, and discuss ways that QuPath can be used – on its own and with other open tools – for a range of bioimage analysis applications.

CellProfiler - lessons from the first 20 years (and plans for a few more than that)

Dr Beth Cimini, Associate Director for Bioimage Analysis, Broad Institute, Cambridge, USA

Nodar Gogoberidze, Principal Software Engineer, Broad Institute, Cambridge, USA

Thursday, 24. April 2025 5 - 6 pm CEST (11 am EDT)

CellProfiler is an open source image analysis workflow creation tool created by Anne Carpenter and Ray Jones in 2003. Now in v4 (with v5 well underway), it has maintained its original mission of allowing biologists of any computational comfort level to create reusable, reproducible image analysis pipelines for a wide variety of tasks. In this seminar, we will discuss the highs and lows of maintaining legacy software, our plans to bring CellProfiler out of a "256x256 world" to better handle modern image data, and our plans to make CellProfiler easier to access from other tools and libraries, as well as to access other tools from CellProfiler's user-friendly interface.

Fiji with Python power: the best of both worlds

Curtis Rueden, research software engineer in the Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, USA

Wednesday, 28. May 2025 @ 10 am CDT / 3 pm UTC/ 5 pm CEST

Duration: 90 minutes

This workshop session will showcase how to harness Fiji/ImageJ's recent capabilities within the Python software ecosystem:

• Invoke Fiji functionality from Python scripts and the Python REPL with PyImageJ.

• Search for and execute Fiji plugins in napari using the napari-imagej plugin.

• Harness the full power of Python in Fiji's Script Editor using Jaunch, Fiji's new launcher.

• Tap into Python-based deep learning from Fiji plugins and scripts using Appose, a new library for interprocess cooperation with shared memory.

Prerequisites for working along:

• A reasonably fast Internet connection

• An up-to-date installation of Fiji from https://fiji.sc/

• Intermediate experience with Fiji/ImageJ and/or with Python scripting

Journey the n-th dimension: past, present, and future of napari

Juan Nunez-Iglesias, Senior Research Fellow / CZI Imaging Software Fellow, Monash eResearch Centre, Australia

Cancelled - NEW DATE will be advertised!  Monday, 23rd of June 2025 @ 10am CET (duration 1 hour)

napari's first commit was in 2018, and was first publicly announced in late 2019. Since then it has become a leading tool for image exploration, annotation, and analysis, particularly for scientists already using the Scientific Python ecosystem. I'll briefly go over napari's design philosophy, then explain where napari has fallen short of those goals, and what's on the roadmap for the future. napari remains a community-developed project and I'll invite attendees to join us in bringing napari's future closer!

Second Topic

Infrastructure for deploying image analysis workflows 

Please find below the information for the second set of GloBIAS seminars starting in November.

Designing and implementing systems to process petabyte scale imaging datasets: Lessons learned

Ankur Kumar, Computational Associate, Broad Institute of MIT and Harvard, Cambridge, USA

Wednesday, 27th of November 2 - 4 pm EST/ 8 - 10 pm CET

Abstract: Biological dataset sizes have increased exponentially in the last decade with no signs of slowing down. Processing these datasets is no longer trivial and requires careful planning and system design.
I will give an overview of the fundamental building blocks for creating such compute pipelines, drawing examples and lessons from my experience managing and processing datasets from the CellPainting Gallery.

NextFlow for Bioimage analysis

Christian Tischer, Team Leader, Data Science Center, EMBL, Heidelberg, Germany

Thursday, 23nd of January 2025 4pm CET (NEW DATE!)

Abstract: Ideally, bioimage analysis workflows should be reproducible, scalable and executable on various compute infrastructures. To this end, a number of bioimage analysts from different institutions started using Nextflow to deploy and share bioimage analysis workflows both locally and on high performance computing platforms. In this seminar, I will introduce Nextflow and show examples for how it can be used in the context of bioimage analysis. 

Image analysis using Galaxy

Beatrix Serrano-Solano, Euro-BioImaging ERIC Bio-Hub, EMBL Heidelberg, Germany

& Anne Fouilloux , Simula Research Laboratory, Oslo, Norway

& Leonid Kostrykin, Biomedical Computer Vision Group, Heidelberg University, BioQuant, IPMB, Heidelberg, Germany

& Ricardo Massei, Helmholtz Center for Environmental Research, UFZ, Leipzig, Germany

Wednesday, 26th of February 2025 2pm to 3:30 pm CET

Abstract: This webinar will introduce the Galaxy Image Analysis Community and highlight our mission to advance the development of FAIR and reproducible image analysis workflows. As part of our commitment to making image data analysis more accessible and collaborative, we will showcase how Galaxy can serve the imaging community. The session will explore Galaxy’s capabilities for integrating popular image analysis tools, interactive environments, and notebooks, making it a versatile platform for researchers across various scientific domains. We will also present how Galaxy facilitates the creation and sharing of reusable workflows, promoting open science and fostering collaboration. To give participants hands-on insight, we’ll provide a live demonstration on designing and running image analysis workflows within Galaxy. 

Previous events:

Large Language Models for Bioimage Analysis 

Exploring how emerging AI technologies can be applied to enhance image analysis tasks.

Large Language Models – an introduction for life scientists

Robert Haase, Image Data Scientist, Lecturer, Training Coordinator, ScaDS.AI / University of Leipzig, Germany

Tuesday 27th August 2024, 3pm - 4pm CEST

Large Language Models (LLMs) are changing the way how humans interact with computers. This has impact on all scientific fields by enabling new ways to achieve for example data analysis goals. In this talk we will go through an introduction to LLMs with respect to applications in the life sciences, softly focusing on bio-imaging. We will learn how to generate text and images using LLMs and how LLMs can extract information from text and images. We will go through selected prompt engineering techniques enabling scientists to tune the output of LLMs towards their scientific goal and how to do quality assurance in this context.

Please check out the follow-up discussion on Image.sc

https://tinyurl.com/482z3edn

BioImage.IO - introduction and application

Caterina Fuster-Barceló, Postdoctoral Researcher, Universidad Carlos III de Madrid, Spain

Friday 27th September 2024, 2pm - 3pm CEST

The dynamic field of bioimage analysis continually seeks innovative tools to democratize access to analysis tools and its documentation. The BioImage.IO Chatbot, leveraging state-of-the-art AI technologies including Large Language Models (LLMs) and Retrieval Augmented Generation (RAG), provides an interactive platform that significantly integrates the exploration and application of bioimage analysis tools and models. This seminar will introduce the BioImage.IO Chatbot's capabilities, focusing on how it facilitates access to advanced analysis tools and documentation, allows for the execution of complex models, and enables users to create customized extensions adjusted to specific research needs. In a live demo, attendees will see how to interact with the chatbot and all its assistants and capabilities. Join us to explore how the BioImage.IO Chatbot ca transform your research by making sophisticated analysis more intuitive and accessible.

Please check out the follow-up discussion on Image.sc

https://tinyurl.com/2v3zr5u7

Exploring how emerging AI technologies can be applied to enhance image analysis tasks.

Harnessing Large Language Models for Bioimage Analysis with Omega

Dr.  Loïc Alain Royer, Senior Group Leader & Director of Imaging AI, Chan Zuckerberg Biohub, USA

Friday 18th of October, 5:30pm - 7pm CEST

Abstract: This seminar will introduce Omega, a tool that utilizes large language models (LLMs) to enhance bioimage analysis. Integrated with the napari viewer, Omega offers a comprehensive range of capabilities including image processing, segmentation, and analysis. Key features include executing Python code, performing web searches, creating custom widgets, and interacting with segmentation algorithms like Cellpose and StarDist. Additionally, Omega can perform image denoising, generate detailed image processing strategies, and visually interpret the napari viewer's contents using LLMs. The tool also includes an AI-augmented code editor for code management and repair, an interactive didactic mode for educational purposes, and support for various coding libraries such as NumPy, scikit-image, and OpenCV. We will discuss challenges like potential errors and the need for careful prompt engineering. Practical examples will demonstrate how to use Omega to make widgets and accelerate the building of bioimage analysis workflows.