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Reposted by Kota Miura

The Francis Crick Institute @crick.ac.uk · 26d

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...

CBIAS napari workshop 2025

www.crick.ac.uk

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Reposted by Kota Miura

BoneJ @bonej.org · 26d

🔥🔥🔥 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 🤞

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Reposted by Kota Miura

Ryan Savill @cryaaa.bsky.social · 26d

(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...

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Reposted by Kota Miura

Daniel Krentzel @danielkrentzel.bsky.social · 28d

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...

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

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Reposted by Kota Miura

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 28d

✍ 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...

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Reposted by Kota Miura

Jean-Yves Tinevez @jytinevez.bsky.social · 28d

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). 👇

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Kota Miura @kbias.bsky.social · 28d

Especially, you can still submit your bioimage analysis question and get your feedback from 140 researchers, many of whom are world-leading experts at call4help session see: call4help.let-your-data-speak.com

Call4help

This is a webpage used to present Image Analysis problems to the broader community.

call4help.let-your-data-speak.com

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Kota Miura @kbias.bsky.social · 28d

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

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Kota Miura @kbias.bsky.social · 28d

we have been working on this for some years and finally out!

Michael Doube @mdoube.bsky.social · Jul 29

📢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

Reposted by Kota Miura

Nicolas Chiaruttini @nkiaru.bsky.social · Jun 18

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...).

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Reposted by Kota Miura

Simon F. Nørrelykke @simonfn.bsky.social · Jul 14

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/

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Reposted by Kota Miura

Saul Kato @focolab.bsky.social · Jul 14

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...

"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

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Reposted by Kota Miura

Jean-Yves Tinevez @jytinevez.bsky.social · Jul 14

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...

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

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Reposted by Kota Miura

Serdar Balci @serdarbalci.com · Jul 13

Using #QuPath with HISTAI SPIDER Colorectal Module
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

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Reposted by Kota Miura

Fabrizio Musacchio @fabmusacchio.bsky.social · Jul 11

✍️ 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

EPFL Brain Mind Institute @epfl-brainmind.bsky.social · Jun 30

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

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

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Reposted by Kota Miura

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · Jul 10

@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)

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

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Reposted by Kota Miura

CCI Uni of Liverpool @cci-liv.bsky.social · Jun 9

‪It has been lovely to meet Kota @kbias.bsky.social after all these years! #imageanalysis @eurobioimaging.bsky.social

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Reposted by Kota Miura

Journal of Cell Science @jcellsci.bsky.social · Jun 5

The application deadline for our next round of 🔬Training Grants is this Friday 6 June.
www.biologists.com/grants/jcs-f...

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Reposted by Kota Miura

the Node @the-node.bsky.social · Jun 6

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:

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

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Reposted by Kota Miura

Joachim Goedhart @joachimgoedhart.bsky.social · Jun 5

I do agree. Well done!

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Reposted by Kota Miura

FocalPlane @focalplane.bsky.social · Jun 5

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...

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

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Kota Miura @kbias.bsky.social · Jun 5

The #quarep-limi wg12 image & analysis publication workshop @ #ELMI2025 quite successful!

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Kota Miura @kbias.bsky.social · Jun 5

Image data & analysis publication check list team ( #quarep-limi wg12) getting ready for the workshop this afternoon
#ELMI2025

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Reposted by Kota Miura

EMBL Events @events.embl.org · Jun 4

Day 2 at #ELMI2025: participants and excibitors enjoying good coffee and conversations ☕🤝

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Reposted by Kota Miura

Gabriel Krens @gkrens.bsky.social · Jun 3

#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/)

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