Mastodawn

"F-BIAS: Towards a distributed national core facility for bioimage analysis", Ambroset et al – with JY Tinevez as corresponding author.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013058

"We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territory and within different research institutions. It attracted and retained analysts thanks to the scientific added value it brought to them. The distributed core facility efficiently addresses the needs of imaging-based research projects, in particular for researchers previously without access to image analysis expertise. It also mitigates the risk of isolation for analyst members that are often the sole expert in image analysis in their local teams. We identify and share the critical components necessary for the success of similar endeavors, to facilitate reproducibility."

#BioimageInformatics #academia

F-BIAS: Towards a distributed national core facility for bioimage analysis †

Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territory and within different research institutions. It attracted and retained analysts thanks to the scientific added value it brought to them. The distributed core facility efficiently addresses the needs of imaging-based research projects, in particular for researchers previously without access to image analysis expertise. It also mitigates the risk of isolation for analyst members that are often the sole expert in image analysis in their local teams. We identify and share the critical components necessary for the success of similar endeavors, to facilitate reproducibility.

Albert Cardona Apr 25, 2025

"Scalable image-based visualization and alignment of spatial transcriptomics datasets", by Preibisch et al. 2025 @preibischs
https://www.sciencedirect.com/science/article/pii/S2405471225000973
#transcriptomics #BioimageInformatics

Albert Cardona Sep 25, 2024

"F-BIAS: Towards a distributed national core facility for Bioimage Analysis", Ambroset et al. 2024 – with Jean-Yves Tinevez at Pasteur.

...where they share their experience in establishing a distributed, nationwide core-facility providing bioimage analysis services to the french scientific community, with the support of France-BioImaging.

https://arxiv.org/abs/2409.15009

#imaging #ScientificFacilities #BioimageInformatics

F-BIAS: Towards a distributed national core facility for Bioimage Analysis

We discuss in this article the creation and organization of a national core facility for bioimage analysis, based on a distributed team. F-BIAS federates bioimage analysts across France and relies on them to deliver services to the researchers of this territory. The main challenge in implementing this structure is to provide significant scientific value to its members, thereby encouraging their active participation and persuading their respective host teams to support their involvement. F-BIAS accomplished this by creating a professional network that mitigates the negative effects of isolation experienced by its members, who are often the sole bioimage analyst within their local teams, and fosters the development of their technical skills. In a second phase we capitalized on F-BIAS to create a virtual, remotely-operating core facility for bioimage analysis, offering consultations and collaborative project services to the scientific community of France. The services are organized so that they also contribute to the technical proficiency of the analysts. To promote the creation of similar structures, we present and discuss here the organization of this nationally distributed bioimage analysis service core, highlighting successes and challenges.

arXiv.org

RoedigerRG Aug 2, 2024

Today Tim gave a quite vibrant presentation of the #biopixR package at our faculty at the #BTUCS. It was great to hear that some colleagues find it useful and want to use it for their research.

#bioimageinformatics #microbeads #microplastic #DNAdamage

RoedigerRG Jul 12, 2024

📊 #rstats is a versatile tool, especially in the field of #Bioinformatics 💻. But how does it fare when it comes to specialization like #bioimageinformatics 🖼️? We're currently working on a review ("Exploring Image Analysis in R: Applications and Advancements") for this. There are many packages 📦 available for various tasks, like our own #biopixR package! In our analysis, we also discovered several packages that were previously unknown to us. More about these will be shared soon! 🚀

Albert Cardona Apr 5, 2024

Image registration for light-microscopy at petabyte scale, an update of the #BigSticher for #FijiSc by @preibischs

https://github.com/JaneliaSciComp/BigStitcher-Spark

Ready for expansion microscopy #ExM approaches to mapping neural circuits and more.

#BioimageInformatics

GitHub - JaneliaSciComp/BigStitcher-Spark: Running compute-intense parts of BigStitcher distributed

Running compute-intense parts of BigStitcher distributed - JaneliaSciComp/BigStitcher-Spark

GitHub

Albert Cardona Apr 5, 2024

From Jan Funke:

How can machine learning help you to analyze your microscopy images?

Find out at the "Deep Learning for Microscopy Image Analysis" course at the #MBL in Woods Hole from Aug 21-Sep 5!

Applications are due April 17.

https://www.mbl.edu/education/advanced-research-training-courses/course-offerings/dlmbl-deep-learning-microscopy-image-analysis

Directed by Jan Funke, Anna Kreshuk and Shalin Mehta, and including Carsen Stringer @computingnature, Florian Jug @florianjug, Martin Weigert, @martinweigert, Virginie Uhlmann @vuhlmann, Alexander Krull, Loïc A. Royer as faculty.

#SummerSchool #academia #WoodsHole #BioimageInformatics

DL@MBL: Deep Learning for Microscopy Image Analysis | Marine Biological Laboratory

The goal of this course is to familiarize researchers in the life sciences with state-of-the-art deep learning techniques for microscopy image analysis and to introduce them to tools and frameworks that facilitate independent application of the learned material after the course.

Marine Biological Laboratory

Albert Cardona Feb 15, 2024

"I would have never thought moving away from a 10yr old JDK could be this smooth!" – Tiago Ferreira, author of the SNT plugin for neuronal tracing among others.

Curtis Rueden pushing forward the release of #FijiSc with #Java21 – a huge upgrade from the decade-old java 8 that Fiji uses today.

Testers are reporting success even in new MacOS chipsets.

https://forum.image.sc/t/jaunch-a-new-java-launcher-test-fiji-with-java-21/92058/1

#ImageProcessing #BioimageInformatics