BioVoxxel (Jan Brocher)
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biovoxxel.de
BioVoxxel (Jan Brocher)
@biovoxxel.de
BioImage Analyst, Consulting, Customized Analysis Programming Founder, PhD in biology, Fiji/ImageJ, Inkscape, Java
🧪🔬💻
🇩🇪 🇬🇧 🇪🇦

Homepage: biovoxxel.de
All relevant BioVoxxel Links: linktr.ee/biovoxxel
LinkedIn Newsletter: http://bit.ly/46mYBL7
Reposted by BioVoxxel (Jan Brocher)
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:
November 20, 2025 at 11:42 AM
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
bit.ly
November 19, 2025 at 9:15 AM
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?...
November 14, 2025 at 11:43 AM
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
November 12, 2025 at 1:06 PM
Reposted by BioVoxxel (Jan Brocher)
#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
September 19, 2025 at 4:08 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
November 10, 2025 at 4:05 PM
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
November 5, 2025 at 9:10 AM
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
October 24, 2025 at 8:01 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
October 22, 2025 at 8:15 AM
Reposted by BioVoxxel (Jan Brocher)
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
October 7, 2025 at 12:39 PM
Reposted by BioVoxxel (Jan Brocher)
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.
October 8, 2025 at 7:57 PM
🔬 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
October 8, 2025 at 8:15 AM
So, now the article also made it into the newsletter and is available!
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
September 24, 2025 at 1:17 PM
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
September 24, 2025 at 8:15 AM
Reposted by BioVoxxel (Jan Brocher)
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.
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...
September 11, 2025 at 8:40 PM
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
September 10, 2025 at 8:15 AM
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!🏃‍♂️
August 30, 2025 at 10:00 PM
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
August 27, 2025 at 8:15 AM
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!🏃‍♂️🏃‍♀️
August 21, 2025 at 6:00 AM
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
August 20, 2025 at 1:00 PM
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
August 13, 2025 at 11:59 PM
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
August 13, 2025 at 8:15 AM
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
July 27, 2025 at 6:43 PM
🎉 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
July 21, 2025 at 7:49 PM
Reposted by BioVoxxel (Jan Brocher)
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...
May 23, 2025 at 1:13 PM