iiinova — where your digital self keeps evolving

BioVoxxel (Jan Brocher) @biovoxxel.de · 02/02/2026

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/...

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BioVoxxel (Jan Brocher) @biovoxxel.de · 03/12/2025

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

linkedin.com

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...

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BioVoxxel (Jan Brocher) @biovoxxel.de · 26/11/2025

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

youtu.be

3D Cell Segmentation and Neighbor Analysis (BioVoxxel)

YouTube video by Jan Brocher

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Jean-Yves Tinevez @jytinevez.bsky.social · 20/11/2025

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:

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BioVoxxel (Jan Brocher) @biovoxxel.de · 19/11/2025

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

bit.ly

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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BioVoxxel (Jan Brocher) @biovoxxel.de · 14/11/2025

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?...

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BioVoxxel (Jan Brocher) @biovoxxel.de · 12/11/2025

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

Basic Microscopic Image Processing and Analysis

ImageJ Macro Scripting for Automatic Image Analysis

From Pixels to Patterns: Applying Machine Learning Tools for Advanced Image Analysis

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Reposted by BioVoxxel (Jan Brocher)

BioImaging North America @bioimagingna.bsky.social · 19/09/2025

#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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 10/11/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 05/11/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 24/10/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 22/10/2025

🧠 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

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Jean-Yves Tinevez @jytinevez.bsky.social · 07/10/2025

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...

forum.image.sc

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...

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Reposted by BioVoxxel (Jan Brocher)

Torsten Wittmann @handle.invalid · 08/10/2025

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.

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BioVoxxel (Jan Brocher) @biovoxxel.de · 08/10/2025

🔬 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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 24/09/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 24/09/2025

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

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Rylie Walsh @ryliewalsh.bsky.social · 11/09/2025

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.

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BioVoxxel (Jan Brocher) @biovoxxel.de · 10/09/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 30/08/2025

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!🏃‍♂️

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BioVoxxel (Jan Brocher) @biovoxxel.de · 27/08/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 21/08/2025

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!🏃‍♂️🏃‍♀️

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BioVoxxel (Jan Brocher) @biovoxxel.de · 20/08/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 14/08/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 13/08/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 27/07/2025

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

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BioVoxxel (Jan Brocher) @biovoxxel.de · 21/07/2025

🎉 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

Image Analysis Automation with ImageJ Macro Scripting

From Pixels to Patterns: Applied Machine Learning Tools for Advanced Image Analysis

Image Analysis Hero Bundle containing 3 courses
1. Basic Microscopic Image Processing and Analysis
2. Image Analysis Automation with ImageJ Macro Scripting
3. From Pixels to Patterns: Applied Machine Learning Tools for Advanced Image Analysis

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Aafke Gros @aafkegros.bsky.social · 23/05/2025

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...

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Robert Haase @haesleinhuepf.bsky.social · 20/05/2025

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...

focalplane.biologists.com

Quality assurance of segmentation results - FocalPlane

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

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Reposted by BioVoxxel (Jan Brocher)

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 01/05/2025

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...

Ad for the Bioimage Analysis Beginnings Bootcamp at the Broad Institute.

Where & When
Broad Institute, 415 Main Street, Cambridge MA (in-person only)
Monday–Friday, August 4–8, 20259:00 AM – 5:00 PM

About the Bootcamp
Learn core bioimage analysis skills using open-source tools for light
microscopy in this hands-on, in-person course. The Bootcamp
covers annotation, segmentation, and deep learning fundamentals.

Fee: $600 (Academic/Non-Profit) | $1000 (Industry/For-Profit)
For more information email ImagingAdmin@broadinstitute.org

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Robert Haase @haesleinhuepf.bsky.social · 25/04/2025

Are you a #BioImageAnalysis pro? Challenge your skills by playing #BIAbubbles! 🎉 Find the right workflows and reproduce the result! 🔬🖥️🕹️ And if you have challenging BIA tasks, new level contributions are welcome! 😀 github.com/haesleinhuep...

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BioVoxxel (Jan Brocher) @biovoxxel.de · 25/04/2025

If you work at a computer all day, nothing beats the tactile joy of offline hobbies—like baking something beautiful and delicious. But if you're deep into image analysis, there's a special kind of reward in automating with ImageJ macros. Different work, different dopamine. Interested in the latter?

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 23/04/2025

Want to hear more about the history of @cellprofiler.bsky.social , and about what comes next? Come listen to @gnodar.bsky.social and I talk about it tomorrow at the @globias.bsky.social seminar series - 5pm CEST/11am CDT/ 8 am PDT. Register NOW (so we have time to send you the link!) at link below!

docs.google.com

GloBIAS seminar series

Please fill out the form if you want to register for our GloBIAS seminar series. The next sessions will be: Wednesday, 26. March 2025 4 - 5 pm CET (3 - 4 pm GMT) Thursday, 24. April 2025 5 - 6 pm CEST...

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BioVoxxel (Jan Brocher) @biovoxxel.de · 23/04/2025

🚀 Tired of manual image analysis or scared of scripting? Our self-paced “ImageJ Macro Scripting for Automatic Image Analysis” course makes automation easy—no coding experience needed! Start from scratch & build pro-level macros. www.biovoxxel.de/individual-w... #ImageJ #MacroScripting

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BioVoxxel (Jan Brocher) @biovoxxel.de · 14/04/2025

Expand your scientific reach by enhancing visual communication. Present your research in a clear, engaging, and easily understandable way - whether in presentations, posters, or publications. Acquire all necessary skills in the Scientific Illustration Inkscape Masterclass. Promo-Code: BUNNY2025

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Wei-Chen CHU @weichen01.bsky.social · 27/03/2025

As a fan of @haesleinhuepf.bsky.social, I had the pleasure of teaching a CLIJ course in Taiwan, as part of our first EABIAS training event. And yes, we are sharing the training materials under a CC-BY license! 🤗 doi.org/10.5281/zeno...

doi.org

Interactive Bioimage Analysis Workflow with CLIJ (@EABIAS 2025 training event)

Presentation file used in the EABIAS training event: EABIAS/2025-ImageJ-Micro-Image-Analysis-and-Programming_Taipei (Lesson_04)Video Recording (in Mandarin): https://www.youtube.com/watch?v=uheSMSENnz...

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BioVoxxel (Jan Brocher) @biovoxxel.de · 26/03/2025

First small step into the future op publication figures. Try the interactive publication figure

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BioVoxxel (Jan Brocher) @biovoxxel.de · 26/03/2025

For a more colorful scientific spring. 🦜🎨💻🔬 The BioVoxxel LUT Channels Tool received a few new standard colors. Check out tools, options and installation BTW: The NEW Scientific Image Editing and Figure Creation online course is coming soon, stay tuned and don't miss! More info and vouchers

The new Biovoxxel channels tool is shown with arrows pointing out the newly added colors. Right of it an image with 3 fluorescent channels is shown displaying a certain combination of some of those colors

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BioVoxxel (Jan Brocher) @biovoxxel.de · 25/03/2025

Subscribe to the BioVoxxel newsletter and get a 10%-OFF voucher for the Scientific Illustration online course. This offer is limited to the first 25 subscribers and only valid until 5th of April. Don't miss your 10% limited saving! Newsletter pop-up on www.biovoxxel.de/individual-w...

Cover image for the Scientific Illustration online workshop. It shows a schematic synapse in overview with a zoomed in view displayed in a circular outline containing molecular structures included fom the PDB protein data base

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BioVoxxel (Jan Brocher) @biovoxxel.de · 05/03/2025

Fantastic NEWS! The successful BioVoxxel workshops will step-by-step become available as online self-learning courses. Scientific Illustration is the first one released and 4 more will follow. Check out the course page: www.biovoxxel.de/individual-w... Enjoy the teaser video youtu.be/qvMHTZAOCrA

youtu.be

Scientific Illustration - An Inkscape Masterclass for Scientists

YouTube video by Jan Brocher

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Biomedical Center Munich / LMU Munich @bmc-lmu.bsky.social · 20/01/2025

An interesting global study on the state of #trust in scientists ⬇️ Worth reading eg where (European) countries stand,how trust differs betw. conservatives and liberals, what scientists should communicate & whether they should be involved in policy-making process. #SciComm #publicengagement #science

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BioVoxxel (Jan Brocher) @biovoxxel.de · 19/12/2024

Thanks for this very nice publication and the comprehensive summary on #imageanalysis trainings. I can fully corroborate it. It is 100% consistent with my own experience over the last 12 years doing full time bioimage analysis workshops for young life scientists. #bia #microscopy #FIJI #biovoxxel

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Reposted by BioVoxxel (Jan Brocher)

Robert Haase @haesleinhuepf.bsky.social · 13/12/2024

Jeey! @nfdi4bioimage.bsky.social published their #RDM-related postcards FAIRly (made by Henning Falk, licensed CC-BY 4.0) 🔬💾😍 github.com/NFDI4BIOIMAG...

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BioVoxxel (Jan Brocher) @biovoxxel.de · 12/12/2024

Digesting some shading, texturing and Geometry Nodes experiments in #Blender. Little test render of an intestine with tissue-like texture and (over-sized 😜) bacteria in schematic toon shader. #SciArt, #SciIllustration, #SciComm

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Helena Klara Jambor @helenajambor.bsky.social · 02/02/2024

Prep a sparkling #GraphicalAbstract Our 10 steps are out 1️⃣ Message 2️⃣ Pics & Pictograms 3️⃣ Charts 4️⃣ lay out Size 5️⃣ Reading Direction 6️⃣ arrange: Arrows 7️⃣ Text 8️⃣ Color 9️⃣ Tools 🔟 Feedback Get in touch for help. #scicomm #phdlife #DataViz #academicwriting 📊🧪 journals.plos.org/ploscompbiol...

3 stages of a GraphicalAbstract / Visual summary / Infographic: top, hand-drawn in black and white, middle, contains color, better annotation, and professional icons, bottom, final stages with pretty colors and creative use of icons.

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BioVoxxel (Jan Brocher) @biovoxxel.de · 07/12/2024

Just listened to a very interesting [Hidden Brain] (open.spotify.com/show/20Gf4IA...) episode on emotional diversity: open.spotify.com/episode/7FBU... A nice example of a interdisciplinary scientific approach holding some enlightening insights.

open.spotify.com

Emotions 2.0: What's Better than Being Happy?

Hidden Brain · Episode

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BioVoxxel (Jan Brocher) @biovoxxel.de · 05/12/2024

#BIAToolTip No.15 On Windows there is the ColourSimulator App which allows you to simulate on your screen with a slidable window to inspect design or images to check if those are inclusive for color deficient vision. The #biovoxxel LUT Channels Tool provides a related functionality.

A screenshot showing the use of the Windows ColourSimulatons app to quickly check color blind friendly display and color usage in images. It shows one image of fluorescently stained cells while combining red, green and blue colors and another one using cyan, yellow and magenta together with the apps sliding window that simulates the color blind vision on screen. Additionally it displays the pop-up menu for the tool.

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