What do we see when looking at cells under the microscope? 👉Some are bigger than others, some are elongated and align with the neighbors & others seem to move. Cool, right? But wouldn't it be cooler to quantify these observations?
I'm @juliaeckert.bsky.social. Let's explore some analysis software!
I'm @juliaeckert.bsky.social. Let's explore some analysis software!
June 8, 2025 at 4:39 PM
Thank you @ucdlibrary.bsky.social for sourcing this fantastice read by @steveroyle.bsky.social for me. Highly recommended for anyone interested in learning more about #cellbiology #biologicalimaging #imageanalysis #datavis also more people should read the #quantixed blog.
January 18, 2026 at 6:24 PM
Thank you @ucdlibrary.bsky.social for sourcing this fantastice read by @steveroyle.bsky.social for me. Highly recommended for anyone interested in learning more about #cellbiology #biologicalimaging #imageanalysis #datavis also more people should read the #quantixed blog.
Ever wondered if analyzing your images by using intensity Z-projections impacts your data?
Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!
buff.ly/KJ147tI
#Microscopy #ZProjection #ImageAnalysis
Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!
buff.ly/KJ147tI
#Microscopy #ZProjection #ImageAnalysis
November 10, 2025 at 4:05 PM
Ever wondered if analyzing your images by using intensity Z-projections impacts your data?
Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!
buff.ly/KJ147tI
#Microscopy #ZProjection #ImageAnalysis
Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!
buff.ly/KJ147tI
#Microscopy #ZProjection #ImageAnalysis
We spend way too much time manually analyzing #microtubules 🔬
Together with Mario, Justus, Dominik, Felix & Erik we used synthetic data and foundation models to build a fully automated segmentation pipeline.
#microscopy, #imageanalysis & #AI
Check out our preprint:
www.biorxiv.org/content/10.6...
Together with Mario, Justus, Dominik, Felix & Erik we used synthetic data and foundation models to build a fully automated segmentation pipeline.
#microscopy, #imageanalysis & #AI
Check out our preprint:
www.biorxiv.org/content/10.6...
January 14, 2026 at 4:33 PM
We spend way too much time manually analyzing #microtubules 🔬
Together with Mario, Justus, Dominik, Felix & Erik we used synthetic data and foundation models to build a fully automated segmentation pipeline.
#microscopy, #imageanalysis & #AI
Check out our preprint:
www.biorxiv.org/content/10.6...
Together with Mario, Justus, Dominik, Felix & Erik we used synthetic data and foundation models to build a fully automated segmentation pipeline.
#microscopy, #imageanalysis & #AI
Check out our preprint:
www.biorxiv.org/content/10.6...
It has been lovely to meet Kota @kbias.bsky.social after all these years! #imageanalysis @eurobioimaging.bsky.social
June 9, 2025 at 8:30 AM
It has been lovely to meet Kota @kbias.bsky.social after all these years! #imageanalysis @eurobioimaging.bsky.social
🔬 Registration is open for our pilot Introduction to napari Workshop!
napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.
#napari #Python #ImageAnalysis #DataScience #OpenSource
napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.
#napari #Python #ImageAnalysis #DataScience #OpenSource
March 11, 2026 at 4:55 AM
🔬 Registration is open for our pilot Introduction to napari Workshop!
napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.
#napari #Python #ImageAnalysis #DataScience #OpenSource
napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.
#napari #Python #ImageAnalysis #DataScience #OpenSource
I put together a small guide on how to get started with Fiji. Please distribute to anyone who might benefit form this! zenodo.org/records/1477... #imageanalysis #fiji #imagej #training
Image handling using Fiji - training materials
Description:This training package provides a guide to image processing and analysis using ImageJ/Fiji, an open-source software widely used in biological and medical imaging. The manual includes step-b...
zenodo.org
January 30, 2025 at 3:10 PM
I put together a small guide on how to get started with Fiji. Please distribute to anyone who might benefit form this! zenodo.org/records/1477... #imageanalysis #fiji #imagej #training
Supercoiling not only brings DNA to life (and makes it dance) but also changes how key proteins such as #CRISPR interact with it. Thanks @qmsmith.bsky.social for the brilliant collaboration, Sylvia for developing an amazing new #imageanalysis pipeline & @eddierollins.bsky.social for beautiful #AFM.
March 25, 2026 at 6:36 PM
Supercoiling not only brings DNA to life (and makes it dance) but also changes how key proteins such as #CRISPR interact with it. Thanks @qmsmith.bsky.social for the brilliant collaboration, Sylvia for developing an amazing new #imageanalysis pipeline & @eddierollins.bsky.social for beautiful #AFM.
If you use Jupyter Notebooks for #ImageAnalysis and would like to explore segmented objects side-by-side with measured features, try out #stackview clusterplot 🖥️🤓
github.com/haesleinhuep...
github.com/haesleinhuep...
November 22, 2024 at 2:30 PM
If you use Jupyter Notebooks for #ImageAnalysis and would like to explore segmented objects side-by-side with measured features, try out #stackview clusterplot 🖥️🤓
github.com/haesleinhuep...
github.com/haesleinhuep...
Keen about High Performance Computing & #imageanalysis? Search for #75 at #ELMI2025 this evening @sebastianmunck.bsky.social @makaefer.bsky.social
June 5, 2025 at 7:03 AM
Keen about High Performance Computing & #imageanalysis? Search for #75 at #ELMI2025 this evening @sebastianmunck.bsky.social @makaefer.bsky.social
🧠 Even in the age of AI, classical image filters still matter!
They reduce noise, preserve edges, and boost segmentation + ML performance.
Filter smart — shape what your algorithm sees.
🔗 Read more: “To filter, or not to filter?” #ImageAnalysis #AI #Microscopy #Segmentation
bit.ly/46mYBL7
They reduce noise, preserve edges, and boost segmentation + ML performance.
Filter smart — shape what your algorithm sees.
🔗 Read more: “To filter, or not to filter?” #ImageAnalysis #AI #Microscopy #Segmentation
bit.ly/46mYBL7
October 22, 2025 at 8:15 AM
🧠 Even in the age of AI, classical image filters still matter!
They reduce noise, preserve edges, and boost segmentation + ML performance.
Filter smart — shape what your algorithm sees.
🔗 Read more: “To filter, or not to filter?” #ImageAnalysis #AI #Microscopy #Segmentation
bit.ly/46mYBL7
They reduce noise, preserve edges, and boost segmentation + ML performance.
Filter smart — shape what your algorithm sees.
🔗 Read more: “To filter, or not to filter?” #ImageAnalysis #AI #Microscopy #Segmentation
bit.ly/46mYBL7
Opus magnum of my former #PhD student @akanksha-jain.bsky.social. She brought the power of #lightsheet imaging to the #Treutlein lab. #Organoids #singlecells #bigdata #imageanalysis You have learned much #Akanksha. You are a #JEDI now. ❤️👏
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Morphodynamics of human early brain organoid development - Nature
Human brain morphodynamics are explored using organoids.
www.nature.com
June 22, 2025 at 3:32 PM
Opus magnum of my former #PhD student @akanksha-jain.bsky.social. She brought the power of #lightsheet imaging to the #Treutlein lab. #Organoids #singlecells #bigdata #imageanalysis You have learned much #Akanksha. You are a #JEDI now. ❤️👏
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Nice shout-out to #opensource #microscopy and #imageanalysis #bioimageanalysis software at #CZIImaging #ImagingTheFuture.
November 13, 2024 at 3:54 PM
Nice shout-out to #opensource #microscopy and #imageanalysis #bioimageanalysis software at #CZIImaging #ImagingTheFuture.
🚨 Deadline extended!
You now have until August 8 to apply for the Light-Sheet Image Analysis Workshop (Jan 5–9, 2026) at Universidad Mayor in Santiago de Chile with the support of CZI @cziscience.bsky.social and @lisium-chile.bsky.social
1/3
You now have until August 8 to apply for the Light-Sheet Image Analysis Workshop (Jan 5–9, 2026) at Universidad Mayor in Santiago de Chile with the support of CZI @cziscience.bsky.social and @lisium-chile.bsky.social
1/3
Light-Sheet Image Analysis Workshop 2026 – lightsheetchile
lightsheetchile.cl
July 28, 2025 at 9:24 AM
Need a 5-15 minute break from doomscrolling? (You know you do!) Take 5 minutes and tell us how to make #bioimageanalysis #imageanalysis better!
Have you ever analyzed a #microscope image before- even just a single one? Please take our survey on progress and places to still improve for image analysis software! #microscopy #imageanalysis #bioimageanalysis forum.image.sc/t/2024-image...
2024 Image Analysis Survey
The Center for Open Bioimage Analysis , Bioimaging North America , the Royal Microscopical Society, and the Global Bioimage Analysts’ Society have now released a new and improved edition of our biannu...
forum.image.sc
November 6, 2024 at 12:05 AM
Need a 5-15 minute break from doomscrolling? (You know you do!) Take 5 minutes and tell us how to make #bioimageanalysis #imageanalysis better!
🌟 Thank you for an amazing #TiM2025! 🌟
Five days filled with inspiring talks, cutting-edge workshops on #microscopy, #RDM, #ImageAnalysis, and much more!
A huge thank you to all 220 participants for your enthusiasm & contributions!
Special thanks to @gerhardholst.bsky.social for the group picture!
Five days filled with inspiring talks, cutting-edge workshops on #microscopy, #RDM, #ImageAnalysis, and much more!
A huge thank you to all 220 participants for your enthusiasm & contributions!
Special thanks to @gerhardholst.bsky.social for the group picture!
March 25, 2025 at 11:48 AM
🌟 Thank you for an amazing #TiM2025! 🌟
Five days filled with inspiring talks, cutting-edge workshops on #microscopy, #RDM, #ImageAnalysis, and much more!
A huge thank you to all 220 participants for your enthusiasm & contributions!
Special thanks to @gerhardholst.bsky.social for the group picture!
Five days filled with inspiring talks, cutting-edge workshops on #microscopy, #RDM, #ImageAnalysis, and much more!
A huge thank you to all 220 participants for your enthusiasm & contributions!
Special thanks to @gerhardholst.bsky.social for the group picture!
I'll be at the Learning Zone at #MMC2025 tomorrow afternoon with @martinjones.bsky.social, @lankylaste.bsky.social & Sara Salgueiro Torres, talking about how you can get started using #OpenSource software like #FIJI, @jupyter.org and @napari.org for #ImageAnalysis
rms-daim.github.io/DAIM-MMC2025/
rms-daim.github.io/DAIM-MMC2025/
June 30, 2025 at 2:03 PM
I'll be at the Learning Zone at #MMC2025 tomorrow afternoon with @martinjones.bsky.social, @lankylaste.bsky.social & Sara Salgueiro Torres, talking about how you can get started using #OpenSource software like #FIJI, @jupyter.org and @napari.org for #ImageAnalysis
rms-daim.github.io/DAIM-MMC2025/
rms-daim.github.io/DAIM-MMC2025/
Ever needed to measure the morphological features of your organism across hundreds of images? 🤯 HusMorph uses #MachineLearning to detect morphological landmarks in the image, speeding up your #ImageAnalysis time!
Read it here: doi.org/10.1093/conp...
Read it here: doi.org/10.1093/conp...
October 24, 2025 at 1:01 PM
Ever needed to measure the morphological features of your organism across hundreds of images? 🤯 HusMorph uses #MachineLearning to detect morphological landmarks in the image, speeding up your #ImageAnalysis time!
Read it here: doi.org/10.1093/conp...
Read it here: doi.org/10.1093/conp...
OUT NOW!
Advances in Digital Archaeology
Proceedings of the 2023 conference Computer Applications and Quantitative Methods in Archaeology – 50 years of synergy
📚 Read online for free or purchase a printed copy at www.sidestone.com/books/advanc...
#digital #3dmodeling #imageanalysis
Advances in Digital Archaeology
Proceedings of the 2023 conference Computer Applications and Quantitative Methods in Archaeology – 50 years of synergy
📚 Read online for free or purchase a printed copy at www.sidestone.com/books/advanc...
#digital #3dmodeling #imageanalysis
April 9, 2026 at 10:10 AM
OUT NOW!
Advances in Digital Archaeology
Proceedings of the 2023 conference Computer Applications and Quantitative Methods in Archaeology – 50 years of synergy
📚 Read online for free or purchase a printed copy at www.sidestone.com/books/advanc...
#digital #3dmodeling #imageanalysis
Advances in Digital Archaeology
Proceedings of the 2023 conference Computer Applications and Quantitative Methods in Archaeology – 50 years of synergy
📚 Read online for free or purchase a printed copy at www.sidestone.com/books/advanc...
#digital #3dmodeling #imageanalysis
I started using #MachineLearning to classify images in #ImageJ : trainable #Weka Segmentation which is great! 3 cycles and I got this:
However, the result image has one channel. Does anyone know how to split 5 (random) colors in #Fiji to make them single channels? #microscopy #imageanalysis #AI
However, the result image has one channel. Does anyone know how to split 5 (random) colors in #Fiji to make them single channels? #microscopy #imageanalysis #AI
January 6, 2025 at 2:55 PM
I started using #MachineLearning to classify images in #ImageJ : trainable #Weka Segmentation which is great! 3 cycles and I got this:
However, the result image has one channel. Does anyone know how to split 5 (random) colors in #Fiji to make them single channels? #microscopy #imageanalysis #AI
However, the result image has one channel. Does anyone know how to split 5 (random) colors in #Fiji to make them single channels? #microscopy #imageanalysis #AI
🌟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
Ready to automate your #microscopy #imageanalysis tasks? Applications are now open for our next "Introduction to Image Analysis" training course, in London at the @crick.ac.uk on October 27th-28th, 2025! 🔬💻
More info ⬇️
www.crick.ac.uk/whats-on/int...
More info ⬇️
www.crick.ac.uk/whats-on/int...
Introduction to image analysis
www.crick.ac.uk
August 6, 2025 at 6:38 PM
Ready to automate your #microscopy #imageanalysis tasks? Applications are now open for our next "Introduction to Image Analysis" training course, in London at the @crick.ac.uk on October 27th-28th, 2025! 🔬💻
More info ⬇️
www.crick.ac.uk/whats-on/int...
More info ⬇️
www.crick.ac.uk/whats-on/int...
Big congrats to @megan-hager.bsky.social on her award for innovation in human & animal health presenting the business model of our #microscopy and #imageanalysis core! 🔬🧪🧠
April 15, 2025 at 9:58 PM
Big congrats to @megan-hager.bsky.social on her award for innovation in human & animal health presenting the business model of our #microscopy and #imageanalysis core! 🔬🧪🧠
The @royalmicrosoc.bsky.social #DataAnalysisInImaging special issue of Journal of Microscopy is out now! onlinelibrary.wiley.com/toc/13652818...
#ImageAnalysis #BioImageAnalysis #RMSDAIM
#ImageAnalysis #BioImageAnalysis #RMSDAIM
Special Issue: Data Analysis in Imaging: Journal of Microscopy: Vol 296, No 3
The <em>Journal of Microscopy</em> is the oldest journal dedicated to the science of microscopy, publishing the latest advances in microscopy techniques and novel areas of application.
onlinelibrary.wiley.com
November 21, 2024 at 3:57 PM
The @royalmicrosoc.bsky.social #DataAnalysisInImaging special issue of Journal of Microscopy is out now! onlinelibrary.wiley.com/toc/13652818...
#ImageAnalysis #BioImageAnalysis #RMSDAIM
#ImageAnalysis #BioImageAnalysis #RMSDAIM
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