@jmutterer.bsky.social
Reposted
The new version of TrackMate, the v8.1 has just been released. It builds upon the recent v8, linked below, and offers two main improvements 👇
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:
It ships many new features, detailed below, but that are articulated around the following:
December 10, 2025 at 1:13 PM
The new version of TrackMate, the v8.1 has just been released. It builds upon the recent v8, linked below, and offers two main improvements 👇
Reposted
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
Customizable FDM-based zebrafish embryo mold for live imaging
www.biorxiv.org/content/10.1...
Work by Marcela and Jaakko in the lab
November 27, 2025 at 6:53 AM
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
Customizable FDM-based zebrafish embryo mold for live imaging
www.biorxiv.org/content/10.1...
Work by Marcela and Jaakko in the lab
Reposted
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
#HappyFluorescenceFriday!
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
September 23, 2025 at 3:48 PM
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
Reposted
Great visibility for #microscopy images from @france-bioimaging.bsky.social platform Montpellier Ressources Imagerie at European Researcher's Night!
D'autres superbes images issues de la plateforme Montpellier Ressources Imagerie facility (MRI) ont été exposées à la Nuit Européenne des chercheuses organisée par Genopolys au Lycée Joffre le 27 Septembre 🎉
@umontpellier.bsky.social
@cnrsoccitanieest.bsky.social
@eurobioimaging.bsky.social
@umontpellier.bsky.social
@cnrsoccitanieest.bsky.social
@eurobioimaging.bsky.social
October 1, 2025 at 1:20 PM
Great visibility for #microscopy images from @france-bioimaging.bsky.social platform Montpellier Ressources Imagerie at European Researcher's Night!
Reposted
Thrilled to share that our article in @jofmicroscopy.bsky.social is now accessible online and as open access! If you wonder how to start the analysis of your images, we propose a decision tree to help identify suitable methods. Just follow the link(s)...
#imageanalysis #bioimaging
#imageanalysis #bioimaging
"From cells to pixels: A decision tree for designing bioimage analysis pipelines" by Elnaz Fazeli, Robert Haase, Michael Doube, Kota Miura & David Legland is free-to-view here: doi.org/10.1111/jmi....
September 29, 2025 at 4:17 PM
Thrilled to share that our article in @jofmicroscopy.bsky.social is now accessible online and as open access! If you wonder how to start the analysis of your images, we propose a decision tree to help identify suitable methods. Just follow the link(s)...
#imageanalysis #bioimaging
#imageanalysis #bioimaging
Reposted
Biscuits, someone has left oil on the 10x again…
Myself
Myself
September 25, 2025 at 6:41 PM
Biscuits, someone has left oil on the 10x again…
Myself
Myself
Reposted
B y the means of Telescopes, there is nothing so far distant but may be represented to our view; and by the help of Microscopes, there is nothing so small, as to escape our enquiry.
Robert Hooke
Robert Hooke
September 25, 2025 at 6:38 PM
B y the means of Telescopes, there is nothing so far distant but may be represented to our view; and by the help of Microscopes, there is nothing so small, as to escape our enquiry.
Robert Hooke
Robert Hooke
Reposted
We see past time in a telescope and present time in a microscope. Hence the apparent enormities of the present.
Victor Hugo
Victor Hugo
September 25, 2025 at 6:16 PM
We see past time in a telescope and present time in a microscope. Hence the apparent enormities of the present.
Victor Hugo
Victor Hugo
Reply with cool microscopy quotes, Jules Girard, 1877, "les plantes étudiées au microscope"
September 25, 2025 at 5:54 PM
Reply with cool microscopy quotes, Jules Girard, 1877, "les plantes étudiées au microscope"
Reposted
A few months ago @eurobioimaging.bsky.social organized the 'Image Data Community Days 2025' during which I could present our work within @france-bioimaging.bsky.social, creating a nationwide, remotely operating core facility for Bioimage Analysis.
youtu.be/xtLHiio8RF0?...
youtu.be/xtLHiio8RF0?...
Towards a nationwide core facility offering bioimage analysis services| Image Analysis session
YouTube video by Euro-BioImaging Communication
www.youtube.com
August 5, 2025 at 12:21 PM
A few months ago @eurobioimaging.bsky.social organized the 'Image Data Community Days 2025' during which I could present our work within @france-bioimaging.bsky.social, creating a nationwide, remotely operating core facility for Bioimage Analysis.
youtu.be/xtLHiio8RF0?...
youtu.be/xtLHiio8RF0?...
Reposted
I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8
Pixi and Napari-Easy-augment-Batch-DL
YouTube video by Brian Northan
youtu.be
July 30, 2025 at 5:31 PM
I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8
Reposted
Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):
GloBIAS: strengthening the foundations of BioImage Analysis
There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...
arxiv.org
July 10, 2025 at 10:23 PM
Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):
Reposted
VACANCY - We’re seeking an Optical Microscopy Support Specialist to join our Bioimaging Platform, to help train users on light microscopes, collaborate on imaging projects and provide technical support.
www.jic.ac.uk/vacancies/op...
Closing date - 11 August 2025
Contract - Full time, indefinite
www.jic.ac.uk/vacancies/op...
Closing date - 11 August 2025
Contract - Full time, indefinite
Optical Microscopy Support Specialist | John Innes Centre
An exciting opportunity has arisen for an Optical Microscopy Support Specialist to join the Bioimaging Platform at the John Innes Centre.
www.jic.ac.uk
July 15, 2025 at 5:51 PM
VACANCY - We’re seeking an Optical Microscopy Support Specialist to join our Bioimaging Platform, to help train users on light microscopes, collaborate on imaging projects and provide technical support.
www.jic.ac.uk/vacancies/op...
Closing date - 11 August 2025
Contract - Full time, indefinite
www.jic.ac.uk/vacancies/op...
Closing date - 11 August 2025
Contract - Full time, indefinite
Reposted
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
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 territo...
journals.plos.org
June 11, 2025 at 8:29 AM
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
Reposted
BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...
May 1, 2025 at 9:22 PM
BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...
Reposted
The FIRST GloBIAS conference is happening in Kobe, Japan, and we launched the webpage and the registration form. Training school, Hackathon, Taggathon, and Symposium with talks, posters, open-source software lounge, call-4-help on stage!
#BioimageAnalysis
#GloBIAS
#BioimageAnalysis
#GloBIAS
GloBIAS #BioimageAnalysis #Conference 2025 – we have opened the registration for our 2025 in-person event. Please check the webpage www.globias.org/activities/b... for more information and the link to the registration form.
April 16, 2025 at 7:53 PM
The FIRST GloBIAS conference is happening in Kobe, Japan, and we launched the webpage and the registration form. Training school, Hackathon, Taggathon, and Symposium with talks, posters, open-source software lounge, call-4-help on stage!
#BioimageAnalysis
#GloBIAS
#BioimageAnalysis
#GloBIAS
Reposted
GloBIAS #BioimageAnalysis #Conference 2025 – we have opened the registration for our 2025 in-person event. Please check the webpage www.globias.org/activities/b... for more information and the link to the registration form.
April 16, 2025 at 7:40 PM
GloBIAS #BioimageAnalysis #Conference 2025 – we have opened the registration for our 2025 in-person event. Please check the webpage www.globias.org/activities/b... for more information and the link to the registration form.
I tricked ChatGPT into helping me create an #ImageJ macro language extension to create/process data in the XML format. It's available here for anyone to use: github.com/mutterer/XML...
March 31, 2025 at 12:09 PM
I tricked ChatGPT into helping me create an #ImageJ macro language extension to create/process data in the XML format. It's available here for anyone to use: github.com/mutterer/XML...
Thank you @gerbi-gmb.de for a wonderful week 💚🔬!
March 24, 2025 at 10:08 AM
Thank you @gerbi-gmb.de for a wonderful week 💚🔬!
Reposted
2 - New support for NGFF images (OME-Zarr, N5, remote or local)
The support for tracking remote images have been completely reworked, based on the N5-universe codebase by @herrsaalfeld.bsky.social lab, with a custom caching strategy.
The support for tracking remote images have been completely reworked, based on the N5-universe codebase by @herrsaalfeld.bsky.social lab, with a custom caching strategy.
January 30, 2025 at 4:44 PM
2 - New support for NGFF images (OME-Zarr, N5, remote or local)
The support for tracking remote images have been completely reworked, based on the N5-universe codebase by @herrsaalfeld.bsky.social lab, with a custom caching strategy.
The support for tracking remote images have been completely reworked, based on the N5-universe codebase by @herrsaalfeld.bsky.social lab, with a custom caching strategy.
Reposted
New Year, new job? Delighted to announce two early-career-level (post-BA/BS or MA) positions in my lab, and an open call for computational postdocs at the Broad!
First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)
First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)
Image analysis associate job description
Image Analysis Associate Broad Institute of MIT and Harvard, Cambridge, MA Impact the discovery of new disease therapies in the Cimini laboratory at the Imaging Platform Join our vibrant, world-clas...
docs.google.com
December 16, 2024 at 3:20 PM
New Year, new job? Delighted to announce two early-career-level (post-BA/BS or MA) positions in my lab, and an open call for computational postdocs at the Broad!
First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)
First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)
Reposted
🌟We are looking for a new member of our image analysis team at the Imaging Core Facility of the Biozentrum in Basel 🌟
Are you passionate about science and technology? Are you interested in bioimaging? Please check the job ad below
#JobOpportunity #ImageAnalysis #DeepLearning
@biozentrum.bsky.social
Are you passionate about science and technology? Are you interested in bioimaging? Please check the job ad below
#JobOpportunity #ImageAnalysis #DeepLearning
@biozentrum.bsky.social
Entry-level position (80 - 100%) for bioimage analysis specialist at the Imaging Core Facility (IMCF) of the Biozentrum, University of Basel
www.biozentrum.unibas.ch/open-positio...
@unibas.ch #Biozentrum #Basel #research #science #joboffer #scientific
www.biozentrum.unibas.ch/open-positio...
@unibas.ch #Biozentrum #Basel #research #science #joboffer #scientific
December 13, 2024 at 10:15 AM
🌟We are looking for a new member of our image analysis team at the Imaging Core Facility of the Biozentrum in Basel 🌟
Are you passionate about science and technology? Are you interested in bioimaging? Please check the job ad below
#JobOpportunity #ImageAnalysis #DeepLearning
@biozentrum.bsky.social
Are you passionate about science and technology? Are you interested in bioimaging? Please check the job ad below
#JobOpportunity #ImageAnalysis #DeepLearning
@biozentrum.bsky.social
Anticipated flood of data of 1.16Gb per day!
December 4, 2024 at 6:32 AM
Anticipated flood of data of 1.16Gb per day!
My first post here to share the important fact that turtle shells can be used to create a wonderful digit font.
December 2, 2024 at 6:55 PM
My first post here to share the important fact that turtle shells can be used to create a wonderful digit font.