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New Community Partner: CAREamics!

New Community Partner: CAREamics!

by Joran Deschamps, Beatriz Serrano-Solano

CAREamics, a library that simplifies using deep-learning denoising algorithms, has joined the BioImage Model Zoo.

With CAREamics, users can improve their analysis pipelines by removing noise from their microscopy images through robust image restoration. By leveraging popular deep learning methods, CAREamics empowers researchers to recover high-quality data from low light or fast imaging,  ensuring lower sample phototoxicity, better quantification, and reproducibility in their experiments.

As a Community Partner, CAREamics now provides ready-to-use models compatible with the BioImage.io model format. 

Discover CAREamics models on the BioImage Model Zoo: https://bioimage.io/#/?partner=careamics&type=application

 

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SpotMax joins the BioImage Model Zoo as a Community Partner

SpotMax joins the BioImage Model Zoo as a Community Partner

by Beatriz Serrano-Solano

We are excited to announce that SpotMax, the advanced image analysis framework, has officially joined the BioImage Model Zoo as a Community Partner! This collaboration allows users to leverage SpotMax for running BioImage.io models, further enhancing its integration into the growing bioimage analysis ecosystem.

SpotMax is renowned for its powerful capabilities in automated spot detection and quantification of microscopy images. With a user-friendly interface and built-in features for cell segmentation and tracking, SpotMax enables researchers to harness the full potential of multi-dimensional datasets.

As part of this partnership, SpotMax now provides ready-to-use models and workflows fully compatible with the BioImage.io model format. These tools are readily accessible through the BioImage Model Zoo, empowering researchers to integrate SpotMax models into their analysis pipelines.

This integration underscores our commitment to fostering collaboration and accessibility in bioimage analysis. By bringing SpotMax into the BioImage Model Zoo, we aim to provide the research community with a richer, more versatile toolkit for tackling diverse challenges in bioimaging.

We are delighted to welcome SpotMax as a Community Partner and can’t wait to see the transformative impact of this partnership. Explore SpotMax models on the BioImage Model Zoo today!

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AI4Life at SPAOM 2024: Bridging Advanced Microscopy and AI-Driven Image Analysis

AI4Life at SPAOM 2024: Bridging Advanced Microscopy and AI-Driven Image Analysis

by Caterina Fuster-Barceló

The Spanish-Portuguese Advanced Optical Microscopy Meeting (SPAOM) 2024 brought together leading experts in optical microscopy and image analysis to foster collaboration and innovation in the field. Held this year in the historic city of Toledo, in the Castilla-La Mancha region, SPAOM once again proved to be a dynamic platform for knowledge exchange, networking, and showcasing cutting-edge advancements.


AI4Life was represented by Arrate Muñoz-Barrutia and Caterina Fuster-Barceló, who played a pivotal role in the event. They hosted an engaging Image Analysis Forum, introducing AI4Life and the BioImage Model Zoo, two initiatives revolutionising the intersection of artificial intelligence and bioimaging. During the forum, participants also learned about the BioImage.IO Chatbot and the BioImage Archive, which are closely linked to AI4Life’s mission to advance open and accessible bioimage analysis tools and datasets.

 

Beyond the forum, Arrate and Caterina immersed themselves in the vibrant SPAOM community, networking with researchers and discovering the remarkable projects spearheaded by other attendees. Their participation highlighted AI4Life’s commitment to fostering collaboration and pushing the boundaries of AI applications in bioimaging.

We are excited to see how the connections and ideas sparked at SPAOM 2024 will continue to shape the future of advanced microscopy and image analysis. Stay tuned for updates on AI4Life’s next steps!

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AI4Life’s Highlights at I2K 2024

AI4Life’s highlights at I2K 2024

by Beatriz Serrano-Solano

AI4Life played an important role at the 2024 Images to Knowledge (I2K) conference, held from October 23-25 at the Human Technopole in Milan. As a major event for experts at the intersection of life sciences and quantitative image analysis, I2K offered AI4Life partners an ideal platform to showcase their latest advancements and community contributions.

AI4Life’s impact began at the organizational level, with the AI4Life scientific coordinators Florian Jug and Anna Kreshuk serving on the scientific organizers committee. The conference also welcomed Ricardo Henriques from Instituto Gulbenkian de Ciência (IGC) – University College London (UCL) as an invited speaker, highlighting AI4Life’s expertise in superresolution microscopy.

IMG_20241025_235937
Hands-on learning with specialised workshops

A series of workshops allowed participants to dive into AI4Life’s practical tools and methods:

  • Building Your Own Chatbot for BioImage Analysis: Opening the series on Wednesday.
  • Accelerating Microscopy Image Annotation with SAMJ Annotator and DL4MicEverywhere: Making your deep learning pipelines flexible, shareable, and reproducible workshops on Thursday, enhancing image annotation speed and flexibility.
  • Friday’s sessions included 4 workshops on BiaPy: deep learning based Bioimage Analysis for all audiences, Recent Advances in ilastik, AI4Life: Empowering BioImaging through the BioEngine, and an Introduction to AI4Life and the BioImage Model Zoo
Poster presentations

AI4Life partners presented two posters:
– BioImage.IO Chatbot: A community-driven AI assistant advancing integrative computational Bioimaging, presented on Wednesday.
– Building Foundations for AI-Driven Bioimage Analysis: Discussing infrastructure and annotation platforms critical for bioimage analysis, shared on Thursday. 

 

We look forward to the next I2K and are excited to contribute further to this inspiring community!

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Summary of the AI4Life 3rd General Assembly

Summary of the AI4Life 3rd General Assembly

by Beatriz Serrano-Solano

The AI4Life 3rd General Assembly, held at Human Technopole in Milan on October 21-22, 2024, brought together project partners and collaborators to discuss advancements, challenges, and future directions in AI-driven image analysis.

Key Highlights

The event started with the welcoming remarks by Dorothea Dörr (AI4Life Project Manager) and John Eriksson (Euro-BioImaging Director General and coordinator of the project), followed by an introductory reflection on AI4Life’s achievements over the past two years by Anna Kreshuk and Florian Jug, scientific coordinators of the project.

 
Session 1 – AI4Life services

The first session focused on demonstrations for creating, uploading, and consuming models.
* Demo 1: Showcased how users can create and upload models via a web interface or programmatically through an API.
* Demo 2: Demonstrated model consumption from bioimage.io, community partner tools, and code environments.
* Demo 3: Emphasized the importance of FAIR principles, highlighting AI-ready datasets, FAIR models, and documentation enhancements.

Session 2 – Work Package updates

Work package leads updated the attendees on infrastructure and user services, with WP6 announcing that AI4Life’s 3rd Open Call will be launched soon.

Session 3 – Additional Work Package Presentations

Presentations from WPs 1, 3, 5, and 7 covering project coordination, direct support, data standards, and outreach.

Research Infrastructure Updates

Brief updates from the partner Research Infrastructures: INSTRUCT-ERIC, EU-OPENSCREEN ERIC, EMPHASIS, and EMBRC-ERIC.

Session 4 – Planning the Future

A forward-looking session exploring upcoming project collaborations with BigPicture and AI4EOSC, along with a panel discussion on project sustainability and post-project impact.


The assembly concluded with plans for year three’s demos, events, and outreach initiatives, with final remarks from Anna Kreshuk and Florian Jug.

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AI4Life in Chemical & Engineering News

AI4Life in Chemical & Engineering News

by Beatriz Serrano-Solano

In October 2024, Chemical & Engineering News explored how artificial intelligence is revolutionizing microscopy and featured AI4Life’s role in bridging the gap between life scientists and AI experts. AI4Life was recognized for making advanced AI tools more accessible to researchers, supporting their diverse needs, and fostering collaboration across disciplines.

Read the full article here.

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AI4Life Denoising Challenge 2024: Results

AI4Life Denoising Challenge 2024: Results

by Vera Galinova, Beatriz Serrano-Solano

The AI4Life Denoising Challenge, which aimed to improve the denoising of microscopy images using deep learning, has been successfully completed. With 104 registrations from 27 countries, the challenge gathered participation from the global scientific community, generating 151 total submissions across four distinct leaderboards featuring different datasets containing one of two noise types. 

What was the challenge about?

Microscopy images are indispensable for biological and medical research, but noise introduced during acquisition can impair image quality and complicate interpretation. The challenge’s focus was the unsupervised denoising task, which, unlike supervised learning, does not require pairs of noisy and clean images, simplifying the real-world application of the algorithms. Researchers applied advanced deep learning algorithms to real-world datasets, aiming to improve image quality while preserving essential features such as edges, textures, and fine details. Find all the information on the challenge at https://ai4life.eurobioimaging.eu/denoising-challenge/

Key statistics

  • Total Participants: 104 registrants from 27 countries
  • Total Submissions: 151
  • Leaderboard Submissions:
  • Structured Noise 1: 17 submissions from 7 participants
  • Structured Noise 2: 7 submissions from 5 participants
  • Unstructured Noise 1: 16 submissions from 7 participants
  • Unstructured Noise 2: 13 submissions from 8 participants

Results by category

Structured Noise 1: Hagen et al (50 total submissions)
 

Name

Affiliation

Algorithm

Result

SI-PSNR

Result

SSIM

Code

1

bensalmon

University of Birmingham

COSDD

31.4847

0.5523

Link to code

2

mcroft

Human Technopole

  N2V

30.8962

0.5534

Link to code

3

shanetoy

Seoul National University

  N2V

30.8406

0.5525

Link to code 
Structured Noise 2: SUPPORT (20  total submissions)
 

Name

Affiliation

Algorithm

Result

SI-PSNR

Result

SSIM

Code

1

bensalmon

University of Birmingham

COSDD

30.4415

0.6278

Link to code

2

a897574323

University of Shanghai for Science and Technology

  N2V

29.7744

0.6112

Link to code

3

edoardogiacomello

Human Technopole

  N2V

28.8547

0.5272

Link to code
Unstructured Noise 1: JUMP (47  total submissions)
 

Name

Affiliation

Algorithm

Result

SI-PSNR

Result

SSIM

Code

1

bensalmon

University of Birmingham

COSDD

35.6282

0.9507

Link to code

2

mcroft

Human Technopole

N2V

35.4957 

0.9413

Link to code

3

edoardogiacomello

Human Technopole

N2V

35.4957

0.9412

Link to code
Unstructured Noise 2: W2S (34 total submissions)
 

Name

Affiliation

Algorithm

Result

SI-PSNR

Result

SSIM

Code

1

bensalmon

University of Birmingham

COSDD

35.6855

0.9163

Link to code

2

edoardogiacomello

Human Technopole

N2V2

35.0505 

0.9025

Link to code

3

edoardogiacomello

Human Technopole

N2V

35.0319 

0.9027

Link to code

What’s next?

The AI4Life Denoising Challenge provided a platform for benchmarking denoising methods across various datasets. The challenge showed how unsupervised deep learning algorithms, like COSDD and N2V, can significantly enhance image quality. The leaderboard results asserted the robustness of these methods across different datasets and noise types. 

We encourage researchers to continue to participate in the challenge through late submissions. Please contact us if you want to participate by submitting your algorithm, and the challenge team will assist you. 

Looking ahead, AI4Life plans to host more challenges soon. Stay tuned for upcoming announcements!

 

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AI4Life joins the AI4Europe Community

AI4Life joins the AI4Europe Community

by Beatriz Serrano-Solano

We are excited to announce that AI4Life has officially joined the AI4Europe community, a collaborative platform dedicated to advancing Artificial Intelligence research and innovation across Europe.

The AI-on-Demand (AIoD) platform serves as a community-driven channel designed to ensure quality, trustworthiness, and explainability in AI solutions. Here are some key benefits:

  • Enhanced collaboration: AI4Life members can engage with peers and experts across various disciplines.
  • Access to resources: The AIoD platform provides a wealth of resources, including datasets, tools, services, and educational courses.
  • Dissemination: the platform provides channels to share research outputs, news updates or forthcoming events.

Explore the AI4Life record at https://www.ai4europe.eu/ai-community/projects/ai4life

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AI4Life joins FAIRsharing

AI4Life joins FAIRsharing

by Beatriz Serrano-Solano

AI4Life has officially joined the FAIRsharing community. By registering our records on FAIRsharing, we are reaffirming our commitment to the FAIR principles, which are crucial for the sustainable management and sharing of data and AI models.

AI4Life’s contributions to FAIRsharing include a set of guidelines and resources designed to operationalize the FAIR principles within the context of AI and bioimaging. Some of the key resources and guidelines now available on FAIRsharing include:

BioImage Model Zoo Model Specification

A standard format for documenting and disseminating AI models, ensuring cross-compatibility with bioimaging tools and easy integration into research workflows. Explore the record here.

Guidelines for AI-Ready Datasets (MIFA)

Detailed guidance on metadata, formats, and accessibility to make datasets AI-ready and compliant with FAIR standards. Explore the record here.

BioImage.IO Repository

The BioImage Model Zoo is community-driven repository of pre-trained AI models. Explore the record here.

AI4Life Collection

All these records are collected under the AI4Life umbrella record. https://fairsharing.org/collection/AI4Life

For more details on our FAIRsharing records and how they can benefit your research, take a look at our recent deliverable:

 https://zenodo.org/records/13618545 

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BioImage.IO Chatbot featured in Nature Methods

BioImage.IO Chatbot featured in Nature Methods

by Beatriz Serrano-Solano

The BioImage.IO Chatbot has been featured in Nature Methods as of August 2024. This tool is designed to make advanced bioimage analysis accessible to researchers at all levels using Large Language Models (LLMs) and Retrieval Augmented Generation (RAG) to offer a user-friendly interface to perform complex image analysis tasks.

To explore its capabilities and learn how it can accelerate your research, check out the full article published on FocalPlane:

BioImage.IO Chatbot: Ready to use and discover!

Read the full article here.