Another outcome from the Appose processing hackathon: Cellpose simple tile processing in Fiji, with #imglib2 and #appose only. With @gaellel.bsky.social and @strigaud.bsky.social
Stéphane Rigaud
@strigaud.bsky.social
Bio-image Analyst, Computer scientist, and plenty of other things that end in «-ist»
The paper is now published in Current Protocols!! 🎉🥳 currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1... Some personal story below 👇 , and technical details in the linked post that featured the preprint 👉
Automated Optimization of Bacterial Tracking Pipelines With TrackMate 8
Quantitative analysis of bacterial dynamics in time-lapse microscopy requires robust tracking pipelines, yet selecting and optimizing algorithms for specific experiments remains challenging. Indeed, ...
currentprotocols.onlinelibrary.wiley.com
Jean-Yves Tinevez@jytinevez.bsky.social · 6mo agoNew preprint alert! We developed an automated framework to optimize tracking pipelines for bacteria, along with a nice integration of tools for bacteria imaging, in the recently released TrackMate 8 (Fiji plugin). www.biorxiv.org/content/10.6... 👇🧵
We are hiring! Join the BioOptics team as a Microscopy Specialist with a focus on multiphoton intravital microscopy. Link below.👇
#HappyFluorescenceFriday #microscopycommunity-Monday is the last day to submit for I2KxBINA 2026! We’re inviting submissions for workshops, talks, and posters for the I2K portion of I2KxBINA 2026, happening Sept 27 to Oct 2, 2026 in Madison, WI. Deadline: May 4, 12pm PT. buff.ly/CBnw1TG
Hi all! 👋 leeboratory.bsky.social and I are recruiting a VIP³ postdoc to join our teams and decode the genetic logic of how blastoids transit to the post-implantation stage. MolBio, genetics and computational approaches. If this sounds like you (or someone you know), we’d love to hear from you! 🚀
leeboratory.bsky.social
Vienna BioCenter Scientific Training@vbcscitraining.bsky.social · 4mo agoWhy choose the Vienna BioCenter - Hear it directly from our fellows! The VIP³ call is open – 8 fully-funded, three-year postdoctoral fellowships in an interdisciplinary environment: https://training.vbc.ac.at/post-docs/vip3-post-doc-program/ #VBCPostDoc
🚨Are you an expert in #proteomics, #metabolomics, #singlecell #spatialomics, or #datascience?🌟 Looking for new opportunities in a growing environment surrounded by scientific excellence (👉 #NIMSB)? And, in Lisbon...🌊🏝️☀️🏄♀️...🍍🦐🍷...❤️ Deadline April 20th👇 www.linkedin.com/posts/nimsb_...
🙌 Programme's out for the Image Data Community Days! Check out the amazing plenary sessions & workshops during our 5-day long online event! There's something for everyone - don't miss out. Registration is FREE & open to all⤵️ www.eurobioimaging.eu/events/image...
We’re looking for a new team member! 🚀 Only 3 more weeks to apply to the fantastic Vienna BioCenter PhD program
Vienna BioCenter Scientific Training@vbcscitraining.bsky.social · 5mo agoOur Spring PhD call is OPEN! 30+ fully funded positions across diverse life science disciplines. Explore projects in Stem Cells, Development: www.vbcphd.at Apply by 9 April 2025 Institute of Molecular Biotechnology, Max Perutz Labs Vienna, IMP, Gregor Mendel Institute of Molecular Plant Biology
Excited to share my first PhD project: LabConstrictor 📒🐍 Have you ever created a Jupyter notebook with all your love 🫶, only for others to be unable to install it 🥲? LabConstrictor, comes to solve this! Check out how it works in the preprint 🔗 arxiv.org/abs/2603.107... or follow this thread ⬇️
Thanks to #Appose hackaton with @jytinevez.bsky.social, @ctrue.bsky.social, @nkiaru.bsky.social, @msphan.bsky.social, @strigaud.bsky.social, Carlos, Thomas and Julie, DeXtrusion can be **INSTALLED** and run to detect cell extrusions directly from Fiji 🤩! Appose is amazing
Let's get ready for a full month of training in image analysis in @pasteur.fr , this summer! Are you interested in learning how to do bioimage analysis? For light microscopy? for cryo-EM? And for cellular cryo-EM? Stay tuned, Pasteur offers access to THREE courses, this June. 👇🎓
Appose processing hackathon with @jytinevez.bsky.social, @ctrue.bsky.social, @gaellel.bsky.social, @strigaud.bsky.social, Carlos and Thomas . Simple POC with Java calling python through Appose to flip blocks. Promising!
One week left to register to the Bioimage Analysis with AI course in Pasteur! This June, 1 - 5. I give a bit more details in the thread below 👇
Institut Pasteur Education@pasteuredu.bsky.social · 5mo ago⚠️ 1 week left for Pasteur Course "Advanced Bioimage Analysis With AI"! 👩🔬💻 Intensive course (June 1-5, Paris): theory + hands-on, AI focus in bioimaging. 📍 Institut Pasteur 🗣️ English ⏰ Deadline: March 1 🔬 Beginner basics, batch scripts, interactive sessions 👉 Apply: https://bit.ly/4c8rFKZ
New preprint alert! We developed an automated framework to optimize tracking pipelines for bacteria, along with a nice integration of tools for bacteria imaging, in the recently released TrackMate 8 (Fiji plugin). www.biorxiv.org/content/10.6... 👇🧵
biorxiv.org
🚨 Job Alert! 🚨 We have an opening at our Microscopy Core Facility in Turku 🇫🇮. If you love imaging 🔬 and helping scientists succeed, we want you! 👇 abo.rekrytointi.com/paikat/index... #Microscopy #ScienceJobs #CoreFacility #Imaging @turkubioscience.bsky.social
Laboratory Engineer (Senior), in Advanced Imaging, 1.5.2026-31.12.2028
abo.rekrytointi.com
I will be recruiting two postdocs early next year. - One image analyst - one biologist interested in working on lymphatics! Reach out if you are interested 👍
Guillaume Jacquemet@guijacquemet.bsky.social · 8mo agoThe Center is a wonderful collaboration with scientists extraordinaire @taijamakinenlab.bsky.social Kari Vaahtomeri and Cecilia Sahlgren. We are all recruiting, so keep an eye on our website If you are looking for a postdoc position 😀
🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
janelia.org
Interested in Zebrafish brain imaging? We released a 3D printed mold that's is super helpful for us. Check it out Customizable FDM-based zebrafish embryo mold for live imaging www.biorxiv.org/content/10.1... Work by Marcela and Jaakko in the lab
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji. It ships many new features, detailed below, but that are articulated around the following:
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr research.pasteur.fr/fr/job/open-...
Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research
Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...
research.pasteur.fr
Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)
Still looking for our perfect doctoral candidate as part of @evomg-dn.bsky.social - come and join us to work on the evolutionary pressures that shape gene expression and disease in the uterus! Please RT (or is it RB? not sure how our lingo has changed!)
EVOMG-Doctoral Network@evomg-dn.bsky.social · 9mo ago🚨 15 days left to apply! Be part of EvoMG-DN and advance your PhD career in evolutionary genomics. 👉 www.evomg-dn.eu #PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions
Hi all. This is the recording of the online seminar I gave following the kind invitation of #GLOBIAS. I share what we have learned delivering #BioimageAnalysis services in the IAH core facility of the @institutpasteur.bsky.social research.pasteur.fr/en/team/imag... ⬇️
Image Analysis Hub - Research
The Image Analysis Hub is an open-access / equal-access core facility committed to sharing bioimage analysis services expertise with the scientific community. What we do The IAH works by collaborating...
research.pasteur.fr
GloBIAS@globias.bsky.social · 10mo agoNew video available in the #GloBIAS YouTube channel - we have uploaded the presentation by Jean-Yves Tinevz from September! tinyurl.com/5yc9p42k
Job alert! We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? See also on the forum: forum.image.sc/t/research-e...
Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA
Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...
forum.image.sc
Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)? Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
GloBIAS@globias.bsky.social · 11mo agoNext #GloBIAS seminar is coming up: join us on 22nd of September, 4 pm CEST to hear from Jean-Yves Tinevez about: The scientific added value of a core-facility dedicated to Bioimage Analysis services. Want to register? -> www.globias.org/activities/b...
Save the date! The @pasteur.fr Pasteur course on image analysis is announced: It will happen from the 1st of June to the 5th 2026. This year there will be only one track: the Early Career Investigator track (beginners). 👇
We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊 Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/