#bioimageinformatics — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #bioimageinformatics, aggregated by home.social.
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"Higher-Order Cell Tracking Transformer", Bragantini et al. 2026 (Loïc Royer's lab).
https://arxiv.org/abs/2607.11754Computer vision done right. This time, to track cells as they divide and move about, in a Petri dish or in a developing animal.
The code: https://github.com/royerlab/hoct
Most improvement is in performance (fewer computer resources needed to do the same job) and in needing less human input.
"Evaluated on the Cell Tracking Challenge and a bacteria division benchmark, HOCT achieves state-of-the-art results without deep pre-trained image encoders."
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"Higher-Order Cell Tracking Transformer", Bragantini et al. 2026 (Loïc Royer's lab).
https://arxiv.org/abs/2607.11754Computer vision done right. This time, to track cells as they divide and move about, in a Petri dish or in a developing animal.
The code: https://github.com/royerlab/hoct
Most improvement is in performance (fewer computer resources needed to do the same job) and in needing less human input.
"Evaluated on the Cell Tracking Challenge and a bacteria division benchmark, HOCT achieves state-of-the-art results without deep pre-trained image encoders."
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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."
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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."
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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.
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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.
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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
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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
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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
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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
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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
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Half way to I2K (Images to Knowledge), hosted by @bethcimini
Now open for workshop proposals.
Dates: November 17-19, 2025
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Half way to I2K (Images to Knowledge), hosted by @bethcimini
Now open for workshop proposals.
Dates: November 17-19, 2025
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"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."
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"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."
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"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 -
"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.
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"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.
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📊 #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! 🚀
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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.
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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.
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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.
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 -
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.
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
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"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
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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.
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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.
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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
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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