Kota Miura

GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile

Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package:

- fully bootstrapped Java setup (just pip install)
- lazy, repeatably-indexable Array object
- fully spec-compliant OME-Zarr group obj.
- xarray/dask exports

github.com/imaging-form...
v0.0.rc1 on PyPI

In September 2024, I was diagnosed with ALS. Today, I can no longer speak, I am confined to a wheelchair, and I can no longer move my arms. It's really shitty. I will write here soon about how I am coping with this and how I am trying to stay cheerful. #ALS

Hi Thorsten, great to hear from you, and how unfair your situation now is... Just to let you know some good news: I recently benchmarked your ridge detection plugin and found it quite robust (the best...) in measuring length. Take care!

fke mail

Warning: another round of fake Kota sending emails to you! Be careful, if the mail address contains "president", it's not from me.

🚀📰 End-of-year news for #RxivMaker =). Now it generates both #pdf and #docx from #markdown. Docx makes it easier to collaborate on a document for non-markdown users, making it simple to loop between docx and #RxivMaker to a professional-looking #preprint

Preprint updated: arxiv.org/abs/2508.00836

Selecting the optimal cell migration assay: fundamentals and practical guidelines - Nature Methods This Review introduces ten cell migration assays, offers practical guidance toward selecting the best assay for a specific biological question and describes how future advances can reveal important in...

To help you select the right assay for a given application, we critically assessed and compared in vitro/in vivo assays to measure cell migration.

Read and use our paper here: www.nature.com/articles/s41...

Contact me if you need a PDF of the paper.

Essentials of Light Microscopy Abstract. Essentials of Light Microscopy gives anyone new to microscopy sufficient information to understand how a light microscope works and how to set it

I came across a new textbook on light microscopy authored by Jeremy Sanderson; it looks like the essence has been extracted from "Understanding Light Microscopy"?
academic.oup.com/book/61662

Also, the PDF or our preprint was created with Rχiv-Maker
@henriqueslab.bsky.social
rxiv-maker.henriqueslab.org

Paper: arxiv.org/html/2508.00...

Anthony A. Hyman will become EMBL’s next Director General.

He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.

www.embl.org/news/people-...

New paper from the @rouxlab.bsky.social on Nature Communications! We study how membrane tension is spatially organized in cells. Using the mechanosensitive probe Flipper-TR to visualize tension across the plasma membrane of adherent cells and to dissect the conditions needed for a gradient to happen

BIOIMAGE ANALYSTS ASSEMBLE!!!

#CBIAS2025

Looks like someone is misusing GloBIAS and its president name to approach people for money transfers. Please note - GloBIAS will always send proper payment requests and has no need for members and volunteers to transfer money on their behalf.

Four men opening sake barrel in a ceremonial way

Opening of the networking dinner by traditional sake opening ceremony
#GloBIAS2025 #BioimageAnalysis @kbias.bsky.social @globias.bsky.social

CBIAS napari workshop 2025

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...

🔥🔥🔥 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 🤞

(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...

✍ 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...

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). 👇

Call4help This is a webpage used to present Image Analysis problems to the broader community.

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

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...

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!

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...).

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/

"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...

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...

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...

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...

GitHub - sbalci/spider-qupath Contribute to sbalci/spider-qupath development by creating an account on GitHub.

Using #QuPath with HISTAI SPIDER Colorectal Module
Repository github.com/sbalci/spide...
Video www.youtube.com/watch?v=8tLO...
#pathsky #digitalpathology #pathology #pathologist

✍️ 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

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...

@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)

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