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Month: March 2024

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Hackathon Summary: BioImage Model Zoo Enhancements

Hackathon Summary: BioImage Model Zoo Enhancements

by Beatriz Serrano-Solano and Joran Deschamps

AI4Life recently organised a hackathon aimed at enhancing the capabilities of the BioImage Model Zoo. Participants from across Europe gathered for a week-long event hosted at EMBL Heidelberg in Germany.

The event kicked off with a round of introductions, allowing participants to outline their personal goals for the week and to form teams that would tackle various project ideas.

Model uploader

One of the key focus areas was to put the final touches to a new model uploader, aimed at simplifying the process of uploading models to the BioImage Model Zoo. The uploader will no longer rely on external platforms like Zenodo; instead, models will be hosted internally and authentication will be requested for contributors who want to upload a model. One of the teams worked to simplify authentication procedures and optimize model uploads to S3 by integrating Google authentication, providing a unified system that would enhance the overall user experience.

Infrastructure improvement

Teams dedicated their efforts to refining Continuous Integration (CI) processes, which have now been migrated to the collection-bioimage-io GitHub repository. The uploader now triggers the CI workflow, automating the process of pushing models to the designated storage location on S3.

JupyterHub and DL4MicEverywhere

Another focus area involved transitioning the infrastructure for JupyterHub from Google Colab to Google Cloud, providing users with a more robust and flexible environment.

Model quantization
Model quantization allows making networks smaller and faster without loss of precision. We held discussions describing current state of the art.. As an example of the performance gains, a 3D Unet model from the BioImage Model Zoo reduced the inference of a batch of images from 60 ms to 30 ms.

Hypha launcher

Hypha can now launch BioEngine (triton-server) on a Slurm cluster using Apptainer. Additionally, a service-id option is now implemented in the BioEngine web client to easily switch the execution backend to high-performance computing (HPC) environments. Furthermore, BioEngine can now be launched on desktop environments.

Model export to new specifications

This team focused on exporting models using the new specifications. Additionally, the team explored approaches to export CellPose models.

Documentation enhancement

This project was split into two phases: firstly, restructuring the current documentation and secondly, creating new needed documentation for the BioImage Model Zoo. Community input and feedback are highly encouraged in this project!

Second Open Call

The deadline for the second Open Call was March 8th. During the hackathon, we had the opportunity to engage with all the reviewers, many of whom were participating in the event. Projects were assigned to each reviewer, kickstarting officially the review process.

Thank you to everyone who contributed either onsite or online. It was a pleasure to work with this engaged group of people. And thank you to the AI4Health innovation cluster for supporting this event. We look forward to meeting you at the next event! 

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Why is the AI4Life Logo a Giraffe? Unraveling the Mystery

Why is the AI4Life Logo a Giraffe? Unraveling the Mystery

by Beatriz Serrano-Solano and Dorothea Dörr

Have you ever wondered why the AI4Life logo is a charming giraffe? Well, you’re not alone! AI4Life decided to host a contest to unravel the mystery, and the responses were so good that we had to pick three winners! Let’s dive into the proposed theories:

Because you’ve got to stand out somehow (both literally and figuratively)

A giraffe represents the essence of evolution and adaptation. Giraffes, with their long necks, have evolved to reach higher, literally and metaphorically. In the context of AI4Life, the giraffe signifies the aspiration for continuous growth and progress. Just like the giraffe adapts to its environment, AI technology continually adapts and evolves to meet new challenges and opportunities. Furthermore, the giraffe's spots could symbolise unique and significant data points. In the world of artificial intelligence, data is invaluable. The spots represent the diverse data sets AI algorithms analyze to gain insights and make decisions. Ultimately, the giraffe logo signifies AI's ability to reach for new horizons, adapt to change, and embrace the complexities of the digital world with grace and innovation. By the way, the colour gradient of the giraffe, transitioning from light green to dark blue, adds a touch of depth. It could signify the spectrum of possibilities AI encompasses, ranging from the initial stages of innovation (light green) to the deep complexities it can explore (dark blue). It's like a journey through the vast landscape of artificial intelligence.

Because we do things so cool, everyone who is not part of us gets a looooong neck… 😉

General Intelligence Requires Artificial Fauna Front Emblem.
With a Giraffe's Reach: Uplifting the Creatures of AI4Life Models to the Cloud. In the innovative landscape, a whimsical giraffe emerged as a symbol of boundless aspirations. Its spots, emblematic of neural networks, and towering neck, represented a conduit to the cloud. This giraffe wasn't just a playful icon, but a tool enabling AI4Life models to transcend the earthly bounds, reaching for the vast computational skies. With the giraffe's assistance, the creatures of AI4Life models soared above the low-hanging fruit, venturing into the expansive realm of cloud computation where innovation knew no bounds. Through the giraffe's reach, every AI model found its passage to the cloud, unlocking a realm of endless exploration and innovation. The narrative finds a whimsical visual representation in this depiction of a giraffe amidst clouds (at https://www.gettyimages.de/fotos/giraffe-in-clouds), symbolizing the limitless voyage AI4Life models undertake with the giraffe's aid to the cloud.

With its long neck, it keeps an overview of all other animals in the zoo.

Because of climate change species are moving north, AI4Life has developed an inclusive adaptation strategy to future climate and welcomes even giraffes incl. the virtual ones.
Well, it all started one day during a brainstorming session. The future AI4Life team was racking their brains trying to come up with a mascot that would perfectly represent their cutting-edge work at the intersection of AI and life sciences. They wanted something that conveyed innovation, adaptability, and, of course, a sense of elegance in the world of biology and imaging. Someone jokingly mentioned that they needed a symbol as unique as a giraffe's neck – able to reach up to those hard-to-reach branches in the data tree. Laughter erupted as people imagined giraffes huddled around microscopes, diligently analysing bioimages with their long necks. They laughed, but then it hit them. The giraffe! A creature known for its exceptional vision, reaching heights that others can only dream of, and demonstrating a remarkable ability to adapt to its environment. Just like their AI algorithms, always reaching for new heights in analysing and understanding life sciences data. They thought, "Why not? Let's embrace the giraffe as a symbol of our willingness to stretch the boundaries of science and technology!" So, the giraffe became the mascot of AI4Life, representing not just their work but also the visionary approach of Euro-BioImaging in advancing the field of bioimaging. And that's how a giraffe ended up in AI4Life's logo, proving that sometimes, in the world of science and AI, the most unexpected inspirations can lead to great discoveries!

AI-generated based on project objectives. ChatGPT or similar.

From all the answers received, 3 winners were selected:

Estibaliz Gomez de Mariscal

FCG-IGC

Being the tallest animal on the earth, the giraffe has the perfect general perspective of what's going around. Thanks to its long neck, it can both, aim to reach the highest appealing branch and get down into the lower details of the animal world. Not only it's a friendly non-predator animal that inspires peacefulness, but rarely other predators attack it, thus becoming a unique symbol of long-standing equilibrium, collaboration and unity for our beloved BioImage Model Zoo.

Caterina Fuster-Barceló

Universidad Carlos III Madrid

To understand why you chose a giraffe as the logo for AI4Life is to consider what makes giraffes special. You might immediately think of their long necks, but the unique aspect that likely inspired this choice is that giraffes communicate through infrasounds, as they are relatively silent animals. This ability allows them to communicate over significant distances. So, when pondering the connection between AI4Life and a giraffe, the commonality lies in the fact that even though partners may be physically distant, they can effectively communicate, akin to the way giraffes do through... infrasounds.

Davide Di Cioccio

EMBRC

It's a reference to the Lamarck theory of evolution: the great effort made on the neck of generations of giraffes (re-iterations of machine learning algorithms) has determined that only the most successful organism (the best algorithm) would find a solution to the problem. Giraffe legs: it's a power plug of a computer.

What a journey of creativity and imagination! From the giraffe’s long neck symbolizing reaching new heights to its unique spots representing valuable data points, the interpretations have been as diverse as they are exciting. Big shoutout to all who joined the fun! And a huge round of applause to our awesome winners!

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AI4Life chosen by the European Commission to be showcased at R&I Research Days 2024

AI4Life chosen by the European Commission to be showcased at R&I Research Days 2024

by Dorothea Dörr and Beatriz Serrano-Solano

AI4Life has been selected by the European Commission Directorate-General for Research and Innovation (RTD) to be showcased at the European Research and Innovation (R&I) Days 2024. The event took place during the Research and Innovation Week on the 20th and 21st of March 2024 in Brussels.

The R&I Days 2024 are an exceptional opportunity for AI4Life to be in the spotlight of policymakers, researchers, stakeholders, and the general public who gathered to discuss and influence the future of research and innovation in Europe and beyond.

For more information, visit the R&I Days 2024 website.

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Euro-BioImaging Virtual Pub session: Tools from AI4Life that anyone can use

Euro-BioImaging Virtual Pub session: Tools from AI4Life that anyone can use

by Beatriz Serrano-Solano

Euro-BioImaging’s Virtual Pub sessions have been a weekly event every Friday since the beginning of the pandemic back in the spring of 2020.
On March 1st, 2024, the session was dedicated to showcasing the tools developed within AI4Life presented by experts among the project partners. Attendees had the opportunity to learn about the BioImage Model Zoo, BioEngine, the BioImage.IO chatbot, and Open Calls and Challenges.

  • Anna Kreshuk, Group Leader at EMBL Heidelberg and scientific coordinator of AI4Life (together with Florian Jug), provided an overview of AI4Life & the BioImage Model Zoo.
  • Wei Ouyang, Assistant Professor at KTH and leader of the AICell Lab at SciLifeLab, Sweden, introduced BioEngine.
  • Caterina Fuster-Barceló, Post-doctoral researcher at Universidad Carlos III de Madrid (UC3M), presented the BioImage.IO chatbot.
  • Vera Galinova, bioimage analyst and research software engineer at Human Technopole, showcased the first Open Call selected projects and future Challenges.

The session recording is now available for public access, so if you missed it, here’s your opportunity to catch up!

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AI4Life project shines at the “Effectively Communicating BioImage Analysis” workshop

AI4Life Project shines at the “Effectively Communicating Bioimage Analysis” workshop

by Caterina Fuster-Barceló and Florian Jug

This past February, the AI4Life project was one of the efforts that took part on the stage at the Effectively Communicating Bioimage Analysis Workshop, held from the 12th to the 15th. Organised by The Company of Biologists and Focal Plane, the event proved to be a resounding success, drawing in members of the AI4Life project alongside a host of other well-established members of our great community.

The workshop served as a critical platform for exchange over some of the bioimage analysis community’s most pressing challenges. 

Among the highlights was the participation of Florian Jug from the HT in Milan, who captivated the audience as one of the invited speakers. Jug presented the AI4Life project and its initiatives, including the BioImage Model Zoo and Open Calls, showcasing the remarkable progress and achievements of the project over recent years. His presentation underscored the project’s efforts in bridging the divide between life scientists and developers, earning widespread admiration for its contributions.

Caterina Fuster-Barceló, representing the Universidad Carlos III de Madrid, Spain, also made significant contributions as part of the early-career researchers funded to attend. Chosen from numerous applications, Caterina represented the deepImageJ team, a Community Partner of the BioImage Model Zoo. She introduced the latest developments of the BioImage.IO Chatbot, a tool designed to address the challenges faced by deepImageJ and bioimage analysis at large.

The workshop not only served as a venue for learning and sharing but also as an opportunity for participants to connect with both new and familiar faces in a friendly and engaging environment. The event’s success reflects the community’s collective effort to foster an atmosphere conducive to growth, collaboration, and fun.

AI4Life stands at the forefront of reducing the gap between AI method development and biological imaging, offering essential services through European transnational and virtual access infrastructures. The project’s participation in the workshop is a testament to its commitment to advancing the field of bioimage analysis, marking yet another milestone in its journey towards integrating AI-based methods into the life sciences.