Kota Miura
@kbias.bsky.social
bioimage analysis, NEUBIAS, GloBIAS
https://www.globias.org/
https://www.globias.org/
Pinned
Kota Miura
@kbias.bsky.social
· Jan 30
GloBIAS: Global BioImage Analysts' society - the idea
YouTube video by GloBIAS
www.youtube.com
what is GloBIAS? here you go...
www.youtube.com/watch?v=LPJE...
www.youtube.com/watch?v=LPJE...
Reposted by Kota Miura
Want to enhance your image analysis skills with napari?
We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.
🕒 Applications close on 15 September.
Learn more and apply 👇
www.crick.ac.uk/whats-on/cbi...
We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.
🕒 Applications close on 15 September.
Learn more and apply 👇
www.crick.ac.uk/whats-on/cbi...
CBIAS napari workshop 2025
www.crick.ac.uk
September 12, 2025 at 10:08 AM
Want to enhance your image analysis skills with napari?
We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.
🕒 Applications close on 15 September.
Learn more and apply 👇
www.crick.ac.uk/whats-on/cbi...
We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.
🕒 Applications close on 15 September.
Learn more and apply 👇
www.crick.ac.uk/whats-on/cbi...
Reposted by Kota Miura
🔥🔥🔥 Upcoming plugin for BoneJ+, Anisotropy+ running on Intel, NVIDIA and AMD GPUs at the same time!
This one uses fields of line probes to determine the fabric tensor and calculate the degree of anisotropy, a measure of underlying texture orientation and scale.
Looking good for release next week 🤞
This one uses fields of line probes to determine the fabric tensor and calculate the degree of anisotropy, a measure of underlying texture orientation and scale.
Looking good for release next week 🤞
September 12, 2025 at 3:43 PM
🔥🔥🔥 Upcoming plugin for BoneJ+, Anisotropy+ running on Intel, NVIDIA and AMD GPUs at the same time!
This one uses fields of line probes to determine the fabric tensor and calculate the degree of anisotropy, a measure of underlying texture orientation and scale.
Looking good for release next week 🤞
This one uses fields of line probes to determine the fabric tensor and calculate the degree of anisotropy, a measure of underlying texture orientation and scale.
Looking good for release next week 🤞
Reposted by Kota Miura
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
September 12, 2025 at 12:44 PM
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
Reposted by Kota Miura
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods
CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...
www.nature.com
September 10, 2025 at 9:37 AM
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Kota Miura
✍ If you're having difficulty writing #BioimageAnalysis code that enables others to follow your workflow, have a look at @haesleinhuepf.bsky.socials slides on „Reproducible Bio-Image Analysis using Python, Napari, Jupyter and AI“ from the #EMBOlsm25.
To the slides: 👉 doi.org/10.5281/zeno...
To the slides: 👉 doi.org/10.5281/zeno...
September 10, 2025 at 12:43 PM
✍ If you're having difficulty writing #BioimageAnalysis code that enables others to follow your workflow, have a look at @haesleinhuepf.bsky.socials slides on „Reproducible Bio-Image Analysis using Python, Napari, Jupyter and AI“ from the #EMBOlsm25.
To the slides: 👉 doi.org/10.5281/zeno...
To the slides: 👉 doi.org/10.5281/zeno...
Reposted by Kota Miura
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
September 10, 2025 at 12:50 PM
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
GloBIAS conference Kobe 2025, the registration for the symposium is still open, until Sept 15th! bit.ly/GloBIAS2025-...
Bioimage Analysis Conference 2025 in Kobe
GloBIAS Bioimage Analysis Conference 2025
Oct 26, 2025 - Oct 31, 2025 | Kobe, Japan
Venue: RIKEN BDR, Kobe, Japan
Registration via Google Forms here:
https://tinyurl.com/3dtajhh6
General informatio...
bit.ly
September 10, 2025 at 8:57 AM
GloBIAS conference Kobe 2025, the registration for the symposium is still open, until Sept 15th! bit.ly/GloBIAS2025-...
we have been working on this for some years and finally out!
📢Accepted manuscript!
From cells to pixels: a decision tree for designing bioimage analysis pipelines.
With @mycroscopy.bsky.social, @haesleinhuepf.bsky.social, @kbias.bsky.social and pushed through by David Legland @inrae-france.bsky.social
Coming soon to J Microsc. @royalmicrosoc.bsky.social
From cells to pixels: a decision tree for designing bioimage analysis pipelines.
With @mycroscopy.bsky.social, @haesleinhuepf.bsky.social, @kbias.bsky.social and pushed through by David Legland @inrae-france.bsky.social
Coming soon to J Microsc. @royalmicrosoc.bsky.social
September 10, 2025 at 8:52 AM
we have been working on this for some years and finally out!
Reposted by Kota Miura
Some rough edges, but it works! #Fiji MCP server (+ Claude desktop) can do things in Fiji (get some info about the current state of the app, execute groovy scripts...).
June 18, 2025 at 6:49 PM
Some rough edges, but it works! #Fiji MCP server (+ Claude desktop) can do things in Fiji (get some info about the current state of the app, execute groovy scripts...).
Reposted by Kota Miura
First day of #bobiac2025. Six days of intensive Python based #BioImageAnalysis. Intro by @fedegasparoli.bsky.social
- "This will be a long week, but it will change your life".
iac.hms.harvard.edu/bobiac/2025/
- "This will be a long week, but it will change your life".
iac.hms.harvard.edu/bobiac/2025/
July 14, 2025 at 1:30 PM
First day of #bobiac2025. Six days of intensive Python based #BioImageAnalysis. Intro by @fedegasparoli.bsky.social
- "This will be a long week, but it will change your life".
iac.hms.harvard.edu/bobiac/2025/
- "This will be a long week, but it will change your life".
iac.hms.harvard.edu/bobiac/2025/
Reposted by Kota Miura
We built StarDist to detect cells in volumetric microscopy and jointly infer closed curved parametric surfaces for each cell. It's an example of an interpretable machine learning approach. More detail in the blog post and preprint.
www.focolab.org/post/surfdis...
www.focolab.org/post/surfdis...
"SurfDist" pre-print posted
We developed an "interpretable machine learning" system to find and characterize blobs in volumetric images, such as microscopy images of cells, something we need to do all the time in our lab. The no...
www.focolab.org
July 14, 2025 at 6:16 PM
We built StarDist to detect cells in volumetric microscopy and jointly infer closed curved parametric surfaces for each cell. It's an example of an interpretable machine learning approach. More detail in the blog post and preprint.
www.focolab.org/post/surfdis...
www.focolab.org/post/surfdis...
Reposted by Kota Miura
Are you developing with TrackMate?
If yes let's get in touch: I plan to make API breaking changes in the future version (v8, soonish) that will break existing detector and segmentation algorithms integration.
Details on the forum: forum.image.sc/t/upcoming-b...
If yes let's get in touch: I plan to make API breaking changes in the future version (v8, soonish) that will break existing detector and segmentation algorithms integration.
Details on the forum: forum.image.sc/t/upcoming-b...
Upcoming breaking changes in TrackMate v8
Hello TrackMate developers, This post is only important if you are developing TrackMate extensions yourself, in particular TrackMate spot detectors and segmentation modules. If not you can skip it en...
forum.image.sc
July 14, 2025 at 8:56 PM
Are you developing with TrackMate?
If yes let's get in touch: I plan to make API breaking changes in the future version (v8, soonish) that will break existing detector and segmentation algorithms integration.
Details on the forum: forum.image.sc/t/upcoming-b...
If yes let's get in touch: I plan to make API breaking changes in the future version (v8, soonish) that will break existing detector and segmentation algorithms integration.
Details on the forum: forum.image.sc/t/upcoming-b...
Reposted by Kota Miura
Using #QuPath with HISTAI SPIDER Colorectal Module
Repository github.com/sbalci/spide...
Video www.youtube.com/watch?v=8tLO...
#pathsky #digitalpathology #pathology #pathologist
Repository github.com/sbalci/spide...
Video www.youtube.com/watch?v=8tLO...
#pathsky #digitalpathology #pathology #pathologist
GitHub - sbalci/spider-qupath
Contribute to sbalci/spider-qupath development by creating an account on GitHub.
github.com
July 13, 2025 at 12:07 PM
Using #QuPath with HISTAI SPIDER Colorectal Module
Repository github.com/sbalci/spide...
Video www.youtube.com/watch?v=8tLO...
#pathsky #digitalpathology #pathology #pathologist
Repository github.com/sbalci/spide...
Video www.youtube.com/watch?v=8tLO...
#pathsky #digitalpathology #pathology #pathologist
Reposted by Kota Miura
✍️ New in #eLife: #CellSeg3D introduces #WNet3D, a self-supervised 3D #segmentation method for #microscopy data — no labels needed. Claims to outperform #Cellpose/#StarDist on 4 datasets. Includes #opensource plugin (#Napari) + full 3D annotated #cortex dataset. Will test it later.
@napari.org
@napari.org
New tool CellSeg3D, from the group of blu.ski/@epfl-brainmind professor Mackenzie Mathis @trackingactions.bsky.social enables self-supervised 3D cell segmentation in fluorescent microscopy,👇 labeling time & 👆quantitative analysis -
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9
Self-supervised, label-free 3D cell imaging is here
EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...
actu.epfl.ch
July 11, 2025 at 1:58 PM
✍️ New in #eLife: #CellSeg3D introduces #WNet3D, a self-supervised 3D #segmentation method for #microscopy data — no labels needed. Claims to outperform #Cellpose/#StarDist on 4 datasets. Includes #opensource plugin (#Napari) + full 3D annotated #cortex dataset. Will test it later.
@napari.org
@napari.org
Reposted by Kota Miura
@kbias.bsky.social, @pmsampaio.bsky.social, @tischi.bsky.social, Rocco D'Antuono, and @haesleinhuepf.bsky.social
did a great job of pulling the data together, to describe who we are, where we want to get, and how we get there together. Check out the preprint and join us today! (5/5)
did a great job of pulling the data together, to describe who we are, where we want to get, and how we get there together. Check out the preprint and join us today! (5/5)
GloBIAS: strengthening the foundations of BioImage Analysis
There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...
arxiv.org
July 10, 2025 at 10:23 PM
@kbias.bsky.social, @pmsampaio.bsky.social, @tischi.bsky.social, Rocco D'Antuono, and @haesleinhuepf.bsky.social
did a great job of pulling the data together, to describe who we are, where we want to get, and how we get there together. Check out the preprint and join us today! (5/5)
did a great job of pulling the data together, to describe who we are, where we want to get, and how we get there together. Check out the preprint and join us today! (5/5)
Reposted by Kota Miura
It has been lovely to meet Kota @kbias.bsky.social after all these years! #imageanalysis @eurobioimaging.bsky.social
June 9, 2025 at 8:30 AM
It has been lovely to meet Kota @kbias.bsky.social after all these years! #imageanalysis @eurobioimaging.bsky.social
Reposted by Kota Miura
The application deadline for our next round of 🔬Training Grants is this Friday 6 June.
www.biologists.com/grants/jcs-f...
www.biologists.com/grants/jcs-f...
June 5, 2025 at 12:34 PM
The application deadline for our next round of 🔬Training Grants is this Friday 6 June.
www.biologists.com/grants/jcs-f...
www.biologists.com/grants/jcs-f...
Reposted by Kota Miura
When it comes to creating plots of your data, are you team 'web apps' or 'vibe coding' with genAI-based tools? 📊
In this post, Joachim Goedhart @joachimgoedhart.bsky.social discusses the potentials and pitfalls of both approaches in data visualization:
In this post, Joachim Goedhart @joachimgoedhart.bsky.social discusses the potentials and pitfalls of both approaches in data visualization:
Visualizing with Vibes: Potential and Pitfalls - the Node
Anyone—regardless of coding skills—should be able to generate a publication-quality plot of their data in minutes. That was the main motivation to develop
thenode.biologists.com
June 6, 2025 at 8:05 AM
When it comes to creating plots of your data, are you team 'web apps' or 'vibe coding' with genAI-based tools? 📊
In this post, Joachim Goedhart @joachimgoedhart.bsky.social discusses the potentials and pitfalls of both approaches in data visualization:
In this post, Joachim Goedhart @joachimgoedhart.bsky.social discusses the potentials and pitfalls of both approaches in data visualization:
Reposted by Kota Miura
I do agree. Well done!
June 5, 2025 at 2:15 PM
I do agree. Well done!
Reposted by Kota Miura
Imaging 4 All - @globalbioimaging.bsky.social have launched their 2nd call for applications.
Researchers from low- and middle-income countries can apply to receive support to visit imaging facilities & attend training courses.
Deadline: 15 August 2025
focalplane.biologists.com/2025/05/20/i...
Researchers from low- and middle-income countries can apply to receive support to visit imaging facilities & attend training courses.
Deadline: 15 August 2025
focalplane.biologists.com/2025/05/20/i...
Imaging 4 All: Funding for Access to Imaging Technologies
Apply to Imaging 4 All (i4A) for fully funded access to bioimaging facilities, laboratories with imaging equipment and imaging-related training worldwide. Open to researchers and imaging scientists ba...
focalplane.biologists.com
June 5, 2025 at 1:42 PM
Imaging 4 All - @globalbioimaging.bsky.social have launched their 2nd call for applications.
Researchers from low- and middle-income countries can apply to receive support to visit imaging facilities & attend training courses.
Deadline: 15 August 2025
focalplane.biologists.com/2025/05/20/i...
Researchers from low- and middle-income countries can apply to receive support to visit imaging facilities & attend training courses.
Deadline: 15 August 2025
focalplane.biologists.com/2025/05/20/i...
The #quarep-limi wg12 image & analysis publication workshop @ #ELMI2025 quite successful!
June 5, 2025 at 2:08 PM
The #quarep-limi wg12 image & analysis publication workshop @ #ELMI2025 quite successful!
Image data & analysis publication check list team ( #quarep-limi wg12) getting ready for the workshop this afternoon
#ELMI2025
#ELMI2025
June 5, 2025 at 9:26 AM
Image data & analysis publication check list team ( #quarep-limi wg12) getting ready for the workshop this afternoon
#ELMI2025
#ELMI2025
Reposted by Kota Miura
#elmi2025 working toward joining forces of builders and creators to share *community tools* @eulimi.bsky.social @bioimagingna.bsky.social -> submit your tool (elmi.embl.org/tools/)
June 3, 2025 at 5:47 PM
#elmi2025 working toward joining forces of builders and creators to share *community tools* @eulimi.bsky.social @bioimagingna.bsky.social -> submit your tool (elmi.embl.org/tools/)
