#Fiji/#ImageJ
Hi Fans of Feedback Microscopy,

what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?

Btw, it works as well in Fiji&ImageJ :-)

Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
November 7, 2025 at 7:23 PM
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...
November 4, 2025 at 10:40 PM
Thanks for doing this! In the wake of the loss of functioning Clear volume in FIJI/ImageJ, I went through a similar process. It is a *GREAT* platform but takes more effort to get started (and render the figures you want) than the easy/WYSIWYG of the ClearVolume GUI.
November 4, 2025 at 12:52 PM
ImageJ/Fiji users will be pleased to know that opening a DICOM stack with File > Import > Image Sequence results in correctly calibrated z pixel spacing.

DICOM slice position (0020,0032) and not slice thickness (0018,0050) fields are used to determine the size of the image stack.
October 27, 2025 at 11:08 AM
...and it’s on the official Fiji/ImageJ documentation! 🥹
October 23, 2025 at 5:33 PM
I’m happy to share some plugins I’ve been developping this summer: "Channels and Contrast" and LUTs Manager!
I can’t find new bugs and ideas by now so I need your help to please test them in your machines and report bugs, feedbacks and ideas! forum.image.sc/t/looking-fo...
October 6, 2025 at 6:52 AM
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 🤩
September 18, 2025 at 9:44 AM
Drop me or @bonej.org a PM for a free token to try out BoneJ's new GPU-accelerated plugins.

All the new commands are in Fiji under Plugins > BoneJ > Plus and are automatically installed and updated when you run the ImageJ Updater (Help > Update...). Work is ongoing - your feedback is essential!
bonej.org BoneJ @bonej.org · Sep 16
📢 GPU-accelerated Anisotropy now in BoneJ+

The fabric tensor expresses the scale and orientation of textures like trabecular bone and other porous materials.

Runs on GPUs from Intel, NVIDIA and AMD, 10-100× faster than the classic version 🔥🔥🔥

Get a token from bonej.org/shop to try it out!
September 16, 2025 at 11:52 AM
It's not yet on the news page (wsr.imagej.net/notes.html) but @wrasband.bsky.social just pushed a new version of ImageJ1 on the servers. Here's the changelog for IJ 1.54q (github.com/imagej/Image...). Use Help>Update ImageJ in IJ or Fiji to upgrade
September 3, 2025 at 11:06 AM
📢 Intel GPUs now supported by BoneJ+ 🤖

Today's new release lets BoneJ+ run on Intel GPUs, which are very common in laptops, in addition to NVIDIA and AMD GPUs. Even antique, 10-year-old ones are working.

Ellipsoid Factor+ is also going 1.5-3× faster.

Just let the ImageJ/Fiji updater run!
September 2, 2025 at 8:24 AM
【生物影像分析入門】AI機器學習與深度學習介紹 — Fiji 影像處理實務報導

本報導整理與說明由臺大顯微影像核心(NTU Imaging Core)發佈之教學內容,主講者羅安琦針對「AI、機器學習(ML)與深度學習(DL)在生物影像分析(BIA)上的應用」做出系統性的介紹與實作示範。文章以新聞報導的語氣呈現要點,並補充背景、技術原理、實務操作建議與常見參數調校策略,方便研究者在使用 ImageJ/Fiji 與相關深度學習工具時有明確的判斷與執行策略。…
【生物影像分析入門】AI機器學習與深度學習介紹 — Fiji 影像處理實務報導
本報導整理與說明由臺大顯微影像核心(NTU Imaging Core)發佈之教學內容,主講者羅安琦針對「AI、機器學習(ML)與深度學習(DL)在生物影像分析(BIA)上的應用」做出系統性的介紹與實作示範。文章以新聞報導的語氣呈現要點,並補充背景、技術原理、實務操作建議與常見參數調校策略,方便研究者在使用 ImageJ/Fiji 與相關深度學習工具時有明確的判斷與執行策略。 本文提要:本課程分為三大部分──(1)AI、機器學習與深度學習的基本觀念與差異;(2)將這些方法整合到生物影像分析流程中的常見工具與平台;(3)三個實務好用的影像分割工具 Labkit、StarDist 與 Cellpose 的操作示範與調參建議。羅安琦在課中強調理論與實作並重,並提供了在 Fiji 平台下結合雲端訓練、本地推論的實務工作流程。 目錄 📌 新聞摘要:AI 與影像分析的核心觀念 🤖 AI、ML、DL 的核心差異與影像應用 🧠 人工神經網路(ANN)與捲積神經網路(CNN)的運作原理 🧾 監督式學習與非監督式學習在影像上的差異 🔬 生物影像分析(BIA)的工作流程與可用工具 ☁️ 平台與雲端資源:何時使用本地,何時使用雲端? 🛠 三款實務分割工具:Labkit、StarDist、Cellpose 概覽與應用情境 🧩 在 Fiji 中實務操作(Labkit 與 CLI 流程) ⚙️ StarDist 與 Cellpose 的參數微調實務建議 🔎 微調與後處理:如何改善分割品質 💡 常見參數解釋與示範實驗結果 🧭 專題建議:選用模型與訓練策略的判斷指引 🧾 範例演示:Cellpose GUI 操作與參數調整 🔗 與其他工具整合:從 Fiji 呼叫外部模型與自動化流程 📚 延伸資源與參考資料
www.isuperman.tw
August 22, 2025 at 9:54 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
LR won't denoise my TIFF files.

Guess tomorrow I get to play "find the plugin for ImageJ/FIJI"

I bet @engineeringjoy.bsky.social can probably do this kind of image processing in her sleep. It is just a bit too much math for me and PS/LR aren't helpful.
July 28, 2025 at 9:42 PM
🏔 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
ImageJ Macro Scripting for Automatic Image Analysis Online Course
YouTube video by Jan Brocher
youtu.be
July 27, 2025 at 6:43 PM
🥾 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
Online Course: Basic Microscopic Image Processing and Analysis Online Course
YouTube video by Jan Brocher
youtu.be
July 27, 2025 at 6:43 PM
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
I'll give it a look, thanks!

Hopefully they gave the tool UI a look; way too many things in imagej don't resize nicely. If I want to widen the levels tool window, for example, the actual active bits don't grow to the new size. Fiji/ImageJ in general just strikes me as a pain in the butt.
July 8, 2025 at 5:32 PM
🚨 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...
July 4, 2025 at 7:57 AM
🔬👨‍💻📰 #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...
July 2, 2025 at 7:09 AM
Two-Point Calibration Protocol for the FRET Indicator Pyronic in Neurons by Alejandro San Martin and team: www.biorxiv.org/content/10.1...
June 25, 2025 at 11:54 AM
Even if you have existing RGB images, in Fiji/ImageJ you can extract each colour and re-assign a more appropriate colour blind friendly colour scheme.
June 19, 2025 at 5:19 PM
🚀 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
June 17, 2025 at 8:16 AM
Zehntausende kann nicht hinkommen, allein wenn man sich die Videos von New York, Chicago und Philadelphia anschaut, was jetzt mit die größten Proteste waren, deren Videos mir begegnet sind. Liebe Tageschau, nehmt ImageJ/Fiji und zählt allein die großen mal richtig durch.
June 15, 2025 at 4:28 PM
.... 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
June 13, 2025 at 10:34 AM