Image analysis is often treated as an individual skill—leading to irreproducible pipelines and bias. Sustainable #BioImageAnalysis must be an institutional responsibility: training, automation, standards, and GSP-aligned guidance. Read the full article on LinkedIn: www.linkedin.com/feed/update/...

To Scale, or not to Scale? - When size matters! "Scaling" in image analysis software like #ImageJ & #Fiji may be used ambiguous for different meanings: - specifying pixel sizes - resizing an image - resizing a selection All of those have different use cases and impact. Read more

No. 09 - To scale, or not to scale?

From pixels, selections, and image sizes - lost in scaling forest When we talk about scaling while working with images for example in ImageJ/Fiji, the word scaling is used for very different processes...

linkedin.com

Beautiful images ≠ usable data. 🎨💻 Ask an image analysis expert BEFORE you start experiments. 20 min prep beats weeks of lost experiments, sweat, tears and frustration. Read more! bit.ly/46mYBL7 Make BioVoxxel your image analyst of choice youtu.be/2Xo7_wQucKk #BioImageAnalysis #Microscopy

3D Cell Segmentation and Neighbor Analysis (BioVoxxel)

YouTube video by Jan Brocher

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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:

To ask, or not to ask? 🎭 already Shakespear knew: “Before thou clicketh ‘Acquire’, consult thy analyst.” Doing image analysis? Check image quality, labels, resolution, metadata with your imaging analyst first — your future self will thank you! Read more: bit.ly/46mYBL7 #Microscopy #BioImaging

Bio-Imaging with Shakespeare | LinkedIn

Biweekly takes on bio-image analysis, processing techniques, insight into tools and trade‑offs as well as best practices

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If you ever heard handpan music, you might have been enchanted by its mesmerizing sound. This is in danger and the handpan might become an "illegal" instrument (if sth. like that ever existed). Please watch the info video and if you feel like and can, help to protect it! youtu.be/6fISj2t0GA8?...

Doing image analysis? You struggle with object extraction, automation, or state-of-the-art ML tools? Want to streamline workflows & get unbiased data! Learn all of that and more with BioVoxxel Online Courses Don't miss out on the expiring 2025 discounts — Enroll NOW! #ImageAnalysis #Microscopy

#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

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

Colocalization isn't just "overlap"—it's potentially 4 distinct analyses or more. Check out how to dissect colocalization analysis and get a glance on pitfalls and methods to report robust colocalization results. Read newsletter now! bit.ly/46mYBL7 #Microscopy #BioImageAnalysis #Colocalization

Happy "#FluorescentFriday", actually luminescence 🌌 🌈 Just feel like sharing some incredible moments recently captured near Tromsø, Norway Experiencing auroras in nature makes me feel tiny and special at the same time. It puts daily life into perspective & sparks huge gratefulness 💚 #Auroras

🧠 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

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

Playing around with how to represent volume in #Snouty light sheet data. Here is a dividing hiPSC with endogenously tagged histone in all three orthogonal projections. Bluer is further away. If anything, it distracts from politics.

🔬 Blinded by colors? Color ≠ Intensity! Quantifying intensities from RGB images (e.g. fluorescence, blots, ...) is mostly misleading! Check your image data type carefully! Learn more in Newsletter No. 5 - To analyze RGB images, or NOT to analyze RGB images? Read and subscribe: bit.ly/46mYBL7

So, now the article also made it into the newsletter and is available!

BioVoxxel (Jan Brocher)@biovoxxel.de · 11mo ago

Bio-Imaging with Shakespeare: pseudocoloring (LUTs) — reveal hidden imaging issues and highlight important data. ✔ Spot noise, shading & saturation ✔ Map data for spatial insight ✔ Make color accessible to all ✔ Why to use a calibration bar Full guide, tools & tutorial inside 👇 buff.ly/8x7Shiq

Bio-Imaging with Shakespeare: pseudocoloring (LUTs) — reveal hidden imaging issues and highlight important data. ✔ Spot noise, shading & saturation ✔ Map data for spatial insight ✔ Make color accessible to all ✔ Why to use a calibration bar Full guide, tools & tutorial inside 👇 buff.ly/8x7Shiq

Everyone who does quantitative microscopy should read this! It’s amazing how many ways we can bias our imaging experiments without realizing we’re doing it.

Journal of Cell Biology@jcb.org · 11mo ago

In 2019, Anna Jost & @jencwaters.bsky.social reviewed best practices for validating quantitative #microscopy methods & discuss strategies to avoid unconscious bias in imaging experiments rupress.org/jcb/article/... 📕 In #Reproducibility & Best Practices in Cell Biology: rupress.org/jcb/collecti...

No. 3 - To Script it, or not to Script it? ImageJ's GenericDialog or ImageJ2 Script Parameter driven dialogs. Which one's for you and fits your needs? BioVoxxel’s latest "Bio-Imaging with Shakespeare" Newsletter explores the trade-offs: buff.ly/8x7Shiq #BioImageAnalysis #ImageJ #SciJava #IJMacro

Amazing BlueSky Summer Sale Last Chance — ONLY 1 DAY LEFT For any of the #BioVoxxel online self-learning courses buff.ly/o64cW9Y Use the code "BSKY101010" at checkout to redeem your discount. Hurry, and see if any codes are left for you! Only 10 codes until August 31st 2025 available!🏃‍♂️

In the 2nd edition of Bio-Imaging with Shakespeare we meet a pesky gremlin — uneven illumination (aka shading, intensity non-uniformity). 🎭🔬 💻 It can quietly bias your segmentation and image analysis results! So, detect it early, correct it appropriately! Subscribe on LinkedIn buff.ly/cLPh8eZ

Amazing BlueSky Summer Sale Your choice: Any of the #BioVoxxel online self-learning courses buff.ly/o64cW9Y The first 10 participants that enroll in the next 10 days get 10% OFF Use the code "BSKY101010" at checkout to redeem your discount. Hurry, only 10 chances until August 31st 2025!🏃‍♂️🏃‍♀️

Embark on your journey to become an #ImageAnalysis champion today! 🏅 🏆 Sign up here: buff.ly/o64cW9Y 1. Basic Microscopic Image Analysis 2. Automate Analyses with #ImageJ #Macro #Scripting 3. Transform Pixels to Patterns with #MachineLearning #Fiji #BioVoxxel Any Questions? -> DM me Bsky

I am stunned! First edition of the "Bio-Imaging with Shakespeare" LinkedIn Newsletter (buff.ly/8x7Shiq) is out for 15h and already 130 subscribers. If you are interested in the topic FOLLOW ME on LinkedIn and Bsky and SUBSCRIBE on LinkedIn buff.ly/cLPh8eZ #bioimageanalysis #biovoxxel #fiji

To interpolate or not to interpolate ? That is the question! 1st edition of the Bio-Imaging with Shakespeare Newsletter I start a biweekly series containing takes on bio-image analysis, processing techniques, insight into tools and trade‑offs as well as best practices. Subscribe buff.ly/cLPh8eZ

In #imageanalysis like in hiking, preparation and training is key to master challenges ahead. 🥾 Hiker: Basic Microscopic Image Processing and Analysis 🏔 Climber: ImageJ Macro Scripting 🧗 Free Climber: Applied #machinelearning Choose your challenge 👉 www.biovoxxel.de/individual-w... #Fiji #ImageJ

🎉 Amazing NEWS for #ImageAnalysis & #LifeSciences folks! The ultimate #imageanalysis #hattrick is here 🧠🔬✨ www.biovoxxel.de/individual-w... Read the 🧵👇 All necessary info and links at the end ! #bioimaging #learning #science #lifescience #microscopy #fiji #imagej #machinelearning #deeplearning

In the context of our @reviewcommons.org revision process, I'm happy to announce Microscopy Nodes v2.2.0! This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more! Preprint at doi.org/10.1101/2025...

I regularly point collaborators at this segmentation quality assurance blog post by @marabuuuu.bsky.social , because some scientists get trapped in a segmentation-improvement-loop without ever measuring how good an algorithm actually is. focalplane.biologists.com/2023/04/13/q...

Quality assurance of segmentation results - FocalPlane

Quality assurance of segmentation results - Bio-image Analysis with Napari

focalplane.biologists.com

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...