Lmst

Half way to I2K (Images to Knowledge), hosted by @bethcimini

Now open for workshop proposals.

Dates: November 17-19, 2025

https://www.i2kconference.org/

"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

"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

"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

Overview of the bioimage analysis services provided by F-BIAS. A. The consultations services take the shape of open-desk sessions of 1 hour organized regularly. A user can book such a session in an online form, providing a description of the image analysis problem they want to discuss, and uploading a few example images. During the preparation phase, the requests are each allocated to an open-desk session, with a panel of 2 to 3 analysts selected according to their expertise. All the sessions happen the same day, with 2 to 3 running in parallel. The analysts join the user in an online meeting of 1 hour and work on the user’s problem during this time, actively prototyping the solutions they propose. The output of a session can be advice on how to address the problem, small analysis pipeline or small macros. B. When a question cannot be addressed in 1 hour and/or requires some development, a user can request a collaborative project, during an open-desk session or by direct contact. Project requests are then evaluated by the F-BIAS team, which estimates the project cost, start delay, and duration. Upon acceptance, an analyst is assigned based on availability and expertise. As a potential opportunity a senior analyst from another site will provide mentoring to the project’s analyst. The user and analyst collaborate asynchronously, with regular analyst reports, using various communication media. Project outputs may include analysis pipelines, results, and reports.

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

📊 #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! 🚀

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

Flow diagram describing the new spark-based BigStitcher software for image registration.

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

"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

From Oliver Burri via #ImageJ mailing list:

SwitZerland’s Image and Data Analysis School #ZIDAS2024

At ETH Zurich from June 23th (Yes, Sunday!) to June 28th 2024.

Are you a life scientist working with microscopy images?
Do you feel like you could use a nudge in the right direction in order to dive into quantitative image analysis ?
Want to learn to program in ImageJ macro language, use novel deep learning tools, discover best practices in image processing all while working on your own data?

The program will focus on hands-on work using the best open source tools available to the BioImage Analysis community.

Registration is open until 2024-03-16.

https://2024.zidas.org
#BioimageInformatics #ImageProcessing

From @florianjug:

#I2K (From Images to Knowledge), the conference where bioimage methods research meets research software engineering meets biology, will welcome you at #HumanTechnopole in Milan from Oct. 23rd to 25th, 2024.

Influence the agenda here: https://docs.google.com/forms/d/e/1FAIpQLSczofxTVbESY60L9eoxEdQxfI7xxpejuphucyfgJpF_pIxdsw/viewform

#BioimageInformatics #ImageProcessing

#BioimageInformatics

Client Info