Day 3️⃣ of our @embo.org course on "Advanced methods in bioimage analysis" at @embl.org with "Practical session 3: Tracking" 🔬🦠🔀.
@jytinevez.bsky.social is already shining at the stage! 🕺🪩.
Important update: #TrackMate v8 is coming! 🤗
@jytinevez.bsky.social is already shining at the stage! 🕺🪩.
Important update: #TrackMate v8 is coming! 🤗
September 16, 2025 at 8:10 AM
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Call 4 Help Pilot Event by GloBIAS, 22 Jan–5 Feb 2025! Offering life scientists a chance for hands-on guidance & support for #bioimage_analysis using Napari, Ilastik & CellProfiler.
💡 Details: www.globias.org/activities/c...
🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...
💡 Details: www.globias.org/activities/c...
🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...
https://forms.gle/7hsJgramrFXBzCjk6]
January 13, 2025 at 1:49 PM
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... a pic kindly taken by Fred Hamprecht who just by chance passed by. Thanks Fred! @ilastik
January 28, 2025 at 7:03 PM
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Huge thanks to the many amazing collaborators: @sulianamanley.bsky.social @anjaliesch.bsky.social @canaztekin.bsky.social @embl.org , @ilastik-team.bsky.social and many others! And thanks to @ritastrack.bsky.social for the excellent paper handling!
June 6, 2025 at 7:06 PM
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At the @training.ebi.embl.org course on Microscopy Data Analysis: Machine Learning & @bioimagearchive.bsky.social, Dominik Kutra from @ilastik-team.bsky.social introduced ilastik and how it supports image analysis. Now, it's time for a hands-on session! 🚀 #BioImageAnalysis #MachineLearning
April 2, 2025 at 8:51 AM
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👇Results from my latest version of desCartes, a hybrid machine learning system for detecting roads on old maps. Its 0.76 IoU score for roads is 31% better than the closest benchmark. 🤯
Preprint forthcoming on arXiv.
Preprint forthcoming on arXiv.
March 30, 2025 at 8:32 PM
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Topics Covered:
Hands-on tutorials and interactive sessions.
Keynotes and collaborative learning.
ECI Track: Fiji, Icy, QuPath, Ilastik, TrackMate, Deep Learning.
Analyst Track: Advanced algorithms, modern tools and image file formats, image analysis for spatial omics, AI in bioimage analysis.
Hands-on tutorials and interactive sessions.
Keynotes and collaborative learning.
ECI Track: Fiji, Icy, QuPath, Ilastik, TrackMate, Deep Learning.
Analyst Track: Advanced algorithms, modern tools and image file formats, image analysis for spatial omics, AI in bioimage analysis.
March 11, 2025 at 2:08 PM
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Otherwise I would try ilastik pixel classification to segment foreground and boundaries of the chromosomes and then use these as the inputs for the interactive watershed. There is also the ilastik carving workflow, which could be used instead of interactive Fiji watershed.
April 8, 2025 at 4:10 PM
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The context-awareness of Spotiflow allows for precise detection in challenging SNR conditions. This includes avoiding artifacts due to e.g. autofluorescence as we show with the beautiful P. dumerilii volumetric smFISH data from the Arendt and @ilastik-team.bsky.social teams @embl.org
(4/N)
(4/N)
June 6, 2025 at 6:58 PM
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Day 1 & 2 of #bobiac2025 🐍
With basics of Python in the bag, it was time to analyze images: image handling, pre-processing, cell segmentation and ilastik.
We could not have organized this course without the generous support of @bioimagingna.bsky.social. Thank you!
With basics of Python in the bag, it was time to analyze images: image handling, pre-processing, cell segmentation and ilastik.
We could not have organized this course without the generous support of @bioimagingna.bsky.social. Thank you!
July 17, 2025 at 12:44 AM
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microscope images. The tools include ilastik, 3D Morph, and Omnipose. I look at how well each one finds the cells and how their results compare. My findings show that each tool sees the cells in its own way, and this can affect the kind of information [2/3 of https://arxiv.org/abs/2505.04838v1]
May 9, 2025 at 5:57 AM
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Necesitas ayuda con analisis de imagenes, desde @globias.bsky.social vamos a ofrecer sesiones de Call4Help. En la encuesta podes llenar si necesitas que la sesion sea en otro idioma y que herramienta preferis (Napari, Ilastik, Fiji, CellProfiler, etc).
docs.google.com/forms/d/e/1F...
docs.google.com/forms/d/e/1F...
GloBIAS Call4Help: Session Feedback and Preferences
Come and get your image analysis questions answered! GloBIAS (globias.org) is organizing virtual community sessions where you can sign up for a time slot to work one-on-one with bioimage analysis expe...
docs.google.com
December 11, 2024 at 9:43 AM
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Indeed, the first thing I tried was Ilastik but I couldn't get it well enough, lots of dark stripes were in the way... In the end it's faster to do it by hand, in this case.
February 3, 2025 at 12:07 PM
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Don’t miss Elena’s (from @ilastik-team.bsky.social lab) brilliant work @ #ICCV2025 with @anwaiarchit.bsky.social & @cppape.bsky.social poster 292 @ 11:15AM 🔬They tackle segmentation of massive 3D microscopy images & show how BatchRenorm removes tiling artifacts boosting transferability and clarity🌺
October 22, 2025 at 8:23 PM
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Tarvittavat työkalut: Python, Ilastik, OpenCV, ImageJ, G'mic, GIMP ja/tai Paint.net.
June 9, 2025 at 9:58 PM
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A new format to ask all you ever wanted to ask about ilastik:
Call 4 Help Pilot Event by GloBIAS, 22 Jan–5 Feb 2025! Offering life scientists a chance for hands-on guidance & support for #bioimage_analysis using Napari, Ilastik & CellProfiler.
💡 Details: www.globias.org/activities/c...
🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...
💡 Details: www.globias.org/activities/c...
🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...
https://forms.gle/7hsJgramrFXBzCjk6]
January 15, 2025 at 9:36 PM
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🚨Está abierta la inscripción para 1ª consultorías de análisis de imágenes de @globias.bsky.social
🔬Sesión piloto con foco en Napari, CellProfiler e Ilastik
🗓️Cupos limitados hasta el viernes 17 de enero
👩🏽💻Expertos latinoamericanos para consultas en español!!
📝Inscripción y detalles
👇
🔬Sesión piloto con foco en Napari, CellProfiler e Ilastik
🗓️Cupos limitados hasta el viernes 17 de enero
👩🏽💻Expertos latinoamericanos para consultas en español!!
📝Inscripción y detalles
👇
Call 4 Help Pilot Event by GloBIAS, 22 Jan–5 Feb 2025! Offering life scientists a chance for hands-on guidance & support for #bioimage_analysis using Napari, Ilastik & CellProfiler.
💡 Details: www.globias.org/activities/c...
🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...
💡 Details: www.globias.org/activities/c...
🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...
https://forms.gle/7hsJgramrFXBzCjk6]
January 14, 2025 at 7:03 PM
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Closing up Day 5 of #TiM2025 with our key note speaker Anna Kreshuk from EMBL @ilastik-team.bsky.social and her vision of & passion for sharing #FAIR data and #machinelearning models in #bioimaging 🔬🖥️⚙️
March 21, 2025 at 8:54 PM
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[ATTENZIONE!]
The grand opening of "The United Forums of Bioimage Analysis"
https://forum.image.sc/
BoneJ
CellProfiler
Cytomine
Fiji
Icy
Ilastik
ImageJ
OpenSPIM
scikit-image
SLIM Curve
... but not limited to these tools.
For ANY questions! #NEUBIAS
The grand opening of "The United Forums of Bioimage Analysis"
https://forum.image.sc/
BoneJ
CellProfiler
Cytomine
Fiji
Icy
Ilastik
ImageJ
OpenSPIM
scikit-image
SLIM Curve
... but not limited to these tools.
For ANY questions! #NEUBIAS
Image.sc Forum
Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).
forum.image.sc
January 28, 2025 at 7:00 PM
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強力な機械学習ベースの生物画像解析マシン、ilastikがFijiのプラグインをリリース。分節化の部分だけiLastikで、みたいなワークフローが作れるようになった。http://ilastik.org/documentation/fiji_export/plugin
January 28, 2025 at 4:09 PM
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We continue the #CBIAS2025 speaker line-up with Dominik Kutra, senior research software engineer in the @ilastik-team.bsky.social. Dominik is one of the core developers of Ilastik, a user-friendly software that leverages machine learning algorithms to easily analyse bioimages
🔗👇
www.ilastik.org
🔗👇
www.ilastik.org
ilastik - ilastik
www.ilastik.org
August 23, 2025 at 9:38 AM
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Kidney Tissue Characterization using Normalized Raman Imaging and Segment-Anything [new]
Analyzes kidney NoRI data via image processing, SAM, Ilastik for automated segmentation, enabling cytoplasm-resolved quantification.
Analyzes kidney NoRI data via image processing, SAM, Ilastik for automated segmentation, enabling cytoplasm-resolved quantification.
October 11, 2025 at 3:06 PM
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Today, #TiM2025 came to a close after a splendid talk by Anna Kreshuk @ilastik-team.bsky.social, Task Area Leader in @nfdi4bioimage.bsky.social, about making machine learning for bioimage analysis not only better but also more accessible.
Thanks to @gerbi-gmb.de for this exciting & inspiring week!
Thanks to @gerbi-gmb.de for this exciting & inspiring week!
March 21, 2025 at 8:51 PM
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先週のNEUBIASではヘッドレスでilastikを使う方法とかを開発者に話してもらった。一連のpyhtonスクリプトをまとめたbashスクリプトにオプションをいろいろつけて使う、という感じ。
January 28, 2025 at 4:09 PM
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