Mastodawn

Florian Jug's lab @florianjug latest:

"MicroSplit: semantic unmixing of fluorescent microscopy data", Ashesh et al. 2026
https://www.nature.com/articles/s41592-026-03082-1

"MicroSplit separates up to four superimposed noisy structures into distinct, denoised image channels, enabling faster and more photon-efficient imaging."

"Built on Variational Splitting Encoder-Decoder networks, models a posterior distribution over solutions, allowing uncertainty-aware predictions and the estimation of spatially resolved prediction errors from posterior variability."

#BioimageInformatics #LightMicroscopy #microscopy

$${\bf{Micro}}{{\mathbb{S}}}{\bf{plit}}$$ Micro S plit : semantic unmixing of fluorescent microscopy data - Nature Methods

$${\rm{Micro}}{\mathbb{S}}{\rm{plit}}$$ M i c r o S p l i t is a computational unmixing method for multiplexed fluorescence imaging of up to four structures per imaging channel.

Nature

Albert Cardona Mar 24

Postdoc position: Career Returner Fellowship

"The LMB is proud to launch a three-year fully funded fellowship for scientists who have had a career break of 12 months or more."

"At the LMB, we understand that stepping away from research – even briefly – can affect career progression. That is why we have created a dedicated postdoctoral fellowship to support researchers who have taken a career break of 12 months or more, for any reason, for example parental leave, health reasons, caregiving, a career change or other personal circumstances."

https://mrclmb.ac.uk/careers-and-people/postdocs/career-returner-fellowship/

Happy to discuss applications to our lab in #Drosophila #connectomics, #ElectronMicroscopy or #ComputerVision applied to #BioimageInformatics.

#MRCLMB #PhDJobs #neuroscience

Career Returner Fellowship | MRC Laboratory of Molecular Biology

Career Returner Fellowship The LMB is proud to launch a three-year fully funded fellowship for scientists who have had a career break of 12 months or more. ...

Albert Cardona Feb 25

Bioimage Analysis course at Pasteur in Paris, by Jean-Yves Tinevez and Jean-christophe Olivo-Marin.

Dates: June 1st-5th, 2026.

Deadline for application: March 1st, 2026.

With two tracks:

* ‘early career investigators track’: aims at mastering the most recent and common image analysis software tools.

* ‘analysts track’: focuses on the use of advanced algorithms and computing resources for bioimage analysis.

https://www.pasteur.fr/en/education/programs-and-courses/pasteur-courses?id_cours=32719

#ImageProcessing #BioimageInformatics #Fiji #Icy #QuPath #Napari #Ilastik #TrackMate

Pasteur courses

Institut Pasteur

Albert Cardona Sep 25, 2025

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

Now open for workshop proposals.

Dates: November 17-19, 2025

https://www.i2kconference.org/

#BioimageInformatics #I2K

Halfway to I2K 2025

From Images to Knowledge

Halfway to I2K 2025

Albert Cardona Jun 11, 2025

"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! 🚀