Latest posts tagged with #ImageJ on Bluesky
The IMAG'IC team is back to offer you the "Introduction to the Use of #ImageJ" training course.
April 09, 2026: Session in French
April 10, 2026: Session in English
institutcochin.fr/formations/f...
@institutcochin.bsky.social
@upcite.bsky.social
@inserm.fr
@cnrs.fr
the same image colorized in greyscale, Rainbow color scale, viridis, and plasma - to show the varying effect of applying color to image on interpretation and visual attention.
Ah, getting nostalgic while making figures for color education!
A former colleague became the new poster child for image tests in computer vision: a test image built in #ImageJ #FIJI
If you are interested, read up on #NewLenna #Lenna, the #metoo moment of CS vision research
#DataVis
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
I updated the Image Viewer and the wiki page with many small bug fixes and features! If you haven't tried it yet, now it's even better ;)
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
My new ImageJ / Fiji toolkit is out 🔥! The goal is to make image handling & visualization easy, with an intuitive interface! Install it on Fiji with the "Image Viewer" update site
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
The IMAG'IC team is back to offer you the "Introduction to the Use of #ImageJ" training course.
October 24, 2025: Session in French
October 29, 2025: Session in English
institutcochin.fr/formations/f...
@institutcochin.bsky.social
@upcite.bsky.social
@inserm.fr
Panoramic view of the classroom waiting for Lecture 6 (Open science and bioimage analysis), while Pavel Tomancak is on screen and Anna Klemm and Christian Tischer are on site organizing the class.
View of the classroom waiting for Lecture 6 (Open science and bioimage analysis) to start, with Pavel Tomancak online.
View of the classroom during Lecture 6 (Open science and bioimage analysis) by Pavel Tomancak online. The screen shows Fiji main plugins and update system.
View of the screens during Lecture 6 (Open science and bioimage analysis) by Pavel Tomancak where we can see "The BIG plan (2007)", with a diagram that goes from Registration to Tracking & Analysis. 2007 and modern pictures of Stephan Preibisch and Stephan Saalfeld are also displayed.
The final lecture of the morning (Lecture 6: Open science and bioimage analysis) is given online by the great @paveltomancak.bsky.social.
We're going through the history of #Fiji and #ImageJ and the big plan behind to Pavel's current projects 🤩
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
Check out my recently published #ImageJ based #opensource tool. It helps clinicians quantify #COVID_19 lung damage from CT scans, providing a reproducible, semi-automatic #analysis crucial for diagnosis. And it works in restricted hospital computer environments! 🩺
Read more: doi.org/10.12688/f10...
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
🏔 Climber: Image Analysis Automation with ImageJ Macro Scripting
Take image analysis automation to the next level. Without any prior programming knowledge, this course will take you the fear if hights and complexity of scripting step-by-step
youtu.be/OaXdxMdaFUE
#ImageJ #Fiji #Macros #Programming
🥾 Hiker: Basic Microscopic Image Processing and Analysis
Learn all the basics of #imagesegmentation to manage flexible #automation of area and object extraction including #qualitycontrol for less bias and reduced errors.
youtu.be/s2T3B5Q8A7c
#ImageJ #Fiji #bioimageanalysis #microscopy
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
2️⃣ Image Analysis Automation with ImageJ Macro Scripting
Tired of doing the same clicks over & over?
This course teaches you to automate your workflows using ImageJ macros.
🛠️ Save time. Get reproducible results. No prior programming skills necessary!
#automation #ImageJ #macro
youtu.be/OaXdxMdaFUE
Basic Microscopic Image Processing and Analysis
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
🎉 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
Raw image (3D)
Cellpose segmentation and applied parameters
CellSeg_3D segmentation and applied parameters
CellSeg_3D post-hoc instant segmentation and applied parameters
Tested both tools also on a more realistic 3D stack from the #ImageJ sample library. #Cellpose is fast and works well out of the box. #CellSeg3D is, however, slower and needs some further tuning for instance segmentation I guess — but looks promising! Definitely worth a try 👌 #BioimageAnalysis
🚨 Important detail in the #ExM & #eSRRF protocol: #eSRRF is not only available as plugin in #ImageJ /Fiji 🌴, #NanoPyx also brings it into the #python world 🐍: doi.org/10.1038/s415...
How to get started? Check out the training manual: doi.org/10.5281/zeno...
🔬👨💻📰 #SReD is out!
Automated structural detection for #ImageJ & #FIJI, from nano to macro ✨🐘. No training data, no bias - texture analysis with GPU acceleration!⚡️
Brainchild of @afonsomendes92.bsky.social and adventure w @christlet.bsky.social lab + friends.
Check: www.nature.com/articles/s41...
This was taken on a @healthcare.nikon.com spinning disc in the core of @nat-prunet.bsky.social. #ImageJ was used for image processing. The LUT was bw_Lagoon (blue) (by
@kwolbachia.bsky.social) for actin and WRA_reddish2 (red) for nuclei.
🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
Per l'estudi, s'han obtingut i analitzat imatges amb el microscopi #confocal Zeiss LSM880 que el Laboratori de Microscòpia Òptica disposa en les instal·lacions #CampusClinic @medicinacs-ub.bsky.social
@zeiss-microscopy.bsky.social #imagej
.... but above all, in times like this, we should act local and help our communities. To protect against anti-science, false promises, and fascism.
Will make more #stickers, until then feel free to re-use my template CC0 FTW
#woodstock #FIJI #Bioimages #ImageJ #BioVis
DEFORM-Net out in npj Artificial Intelligence — an #open-source, unsupervised deep learning tool for full-field displacement estimation in microscopy videos with #ImageJ #FIJI plugin.
Led by Philip Wijesinghe & Soloman Warsop — huge congratulations to the whole team!
www.nature.com/articles/s44...
Try it yourself! The plugin, documentation, and example datasets are available at:
multichannel-nuclear-analysis.github.io
Special thanks to the StarDist team for their incredible segmentation algorithm that made this possible.
#ImageAnalysis #FIJI #ImageJ #Microscopy
One region magnified below — the detail you can achieve with Airyscan is just fantastic! @zeiss-microscopy.bsky.social
Shout out to the core: @nat-prunet.bsky.social
& the LUT-maker: @kwolbachia.bsky.social
#FluorescenceFriday #cellbio #microscopy #devbio #fiji #imagej
🚨 New publication in Star Protocols @cp-starprotocols.bsky.social
A step-by-step #protocol to quantify Yersinia pestis colonization in the #flea Xenopsylla cheopis using #fluorescence #microscopy & #ImageJ.
@ciilofficiel.bsky.social @plbs-lille.bsky.social
#plague #microbiology #OpenAccess
![Error code saying:
[INFO] Version of TensorFlow: TF 1.12.0 CPU
[ERROR] Could not create input stream:
java.io.IOException: HTTP connection failure, errorcode: 403
at org.scijava.io.http.HTTPHandle.result(HTTPHandle.java:192)
at org.scijava.io.http.HTTPHandle.in(HTTPHandle.java:93)
at org.scijava.io.handle.StreamHandle.read(StreamHandle.java:149)
at org.scijava.io.handle.DataHandle.read(DataHandle.java:446)
at org.scijava.io.handle.DataHandles.copy(DataHandles.java:246)
at org.scijava.io.handle.DataHandles.copy(DataHandles.java:191)
at org.scijava.io.handle.DataHandles.copy(DataHandles.java:151)
at org.scijava.download.DefaultDownloadService.lambda$download$1(DefaultDownloadService.java:108)
at org.scijava.task.DefaultTask.lambda$initFuture$0(DefaultTask.java:236)
at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:233)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:750)
and so on...](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:4bzbwekunhj4onto6kjjen7p/bafkreihkk3ofejhwweexwazwi5jpovd2iccgnbzwu6v6n7xiq3oymw4gtq)
Error code saying: [INFO] Version of TensorFlow: TF 1.12.0 CPU [ERROR] Could not create input stream: java.io.IOException: HTTP connection failure, errorcode: 403 at org.scijava.io.http.HTTPHandle.result(HTTPHandle.java:192) at org.scijava.io.http.HTTPHandle.in(HTTPHandle.java:93) at org.scijava.io.handle.StreamHandle.read(StreamHandle.java:149) at org.scijava.io.handle.DataHandle.read(DataHandle.java:446) at org.scijava.io.handle.DataHandles.copy(DataHandles.java:246) at org.scijava.io.handle.DataHandles.copy(DataHandles.java:191) at org.scijava.io.handle.DataHandles.copy(DataHandles.java:151) at org.scijava.download.DefaultDownloadService.lambda$download$1(DefaultDownloadService.java:108) at org.scijava.task.DefaultTask.lambda$initFuture$0(DefaultTask.java:236) at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:233) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:750) and so on...
I am slowly loosing my mind over this #Fiji / #ImageJ plugin...
I want to use Noise2Noise, but it keeps giving me this error code 403... I checked the internet but couldn't find anything that helped me in this situation. I am sure swarm intelligence here knows the issue 😀
#cellbio #microscopy
