Kota Miura
@kbias.bsky.social
📤 195
📥 116
📝 1357
bioimage analysis, NEUBIAS, GloBIAS
https://www.globias.org/
pinned post!
what is GloBIAS? here you go...
www.youtube.com/watch?v=LPJE...
loading . . .
GloBIAS: Global BioImage Analysts' society - the idea
YouTube video by GloBIAS
https://www.youtube.com/watch?v=LPJEh9qT76g
about 1 year ago
0
4
0
Interesting discussion here: analyst-analyst variability of analysis results.
forum.image.sc/t/does-imari...
loading . . .
Does Imaris/Arivis/Aivia reduce inter-analyst variability vs ImageJ/Python/Cellprofiler?
Hi @bcimini I wouldn’t fully rely on these numbers yet, as I still need to clarify a few details with the original authors and make sure there isn’t something I’m overlooking. So far I haven’t been a...
https://forum.image.sc/t/does-imaris-arivis-aivia-reduce-inter-analyst-variability-vs-imagej-python-cellprofiler/119729/24
7 days ago
0
1
0
reposted by
Kota Miura
Anthropic {bot}
7 days ago
Introducing the Anthropic Science Blog. Increasing the pace of scientific progress is a core part of Anthropic’s mission. The Science Blog will feature new research and stories of how scientists are using AI to accelerate their work. Read the intro:
loading . . .
Introducing our Science Blog
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
https://www.anthropic.com/research/introducing-anthropic-science
1
41
11
reposted by
Kota Miura
Crick BioImage Analysis Symposium
about 1 month ago
📣We’re back 🔬👀🖥️!
#CBIAS2026
returns 23–24 November 2026: Join the bioimage analysis community to discuss advances in quantitative imaging & computational methods for image analysis. Great opportunity for early-career analysts & microscopists to present and connect.
#CBIAS2026
#BioimageAnalysis
loading . . .
Crick BioImage Analysis Symposium 2026
https://www.crick.ac.uk/whats-on/crick-bioimage-analysis-symposium-2026
0
15
12
reposted by
Kota Miura
Ian Bogost
about 1 month ago
Is this bad
loading . . .
Einstein - AI Homework Agent
Einstein logs into Canvas and does your homework automatically. He has his own computer — he can watch lectures, read essays, write papers, and participate in discussions.
https://companion.ai/einstein
157
1420
933
reposted by
Kota Miura
Jean-Yves Tinevez
about 1 month ago
One week left to register to the Bioimage Analysis with AI course in Pasteur! This June, 1 - 5. I give a bit more details in the thread below 👇
add a skeleton here at some point
1
40
30
reposted by
Kota Miura
Eugene Katrukha 🇺🇦
about 1 month ago
In the
#BigVolumeBrowser
news, there is a new awesome video tutorial about it made by certified magician Johanna M. Dela Cruz. Check it out:
www.youtube.com/watch?v=c0fr...
(1/2)
loading . . .
Interactive 3D Visualization of Multiple Volumes & Shapes in FIJI (BigVolumeBrowser)
YouTube video by Johanna M. Dela Cruz
https://www.youtube.com/watch?v=c0frU3WpfwE
3
20
10
reposted by
Kota Miura
Talley Lambert
about 1 month ago
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
loading . . .
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
https://github.com/imaging-formats/bffile
1
60
26
reposted by
Kota Miura
Thorsten Wagner
about 1 month ago
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
6
20
7
Warning: another round of fake Kota sending emails to you! Be careful, if the mail address contains "president", it's not from me.
about 1 month ago
1
1
0
reposted by
Kota Miura
Ricardo Henriques
3 months ago
🚀📰 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
1
22
9
reposted by
Kota Miura
Denis Wirtz
3 months ago
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.
loading . . .
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...
https://www.nature.com/articles/s41592-025-02890-1
0
18
4
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
loading . . .
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
https://academic.oup.com/book/61662
3 months ago
0
0
0
reposted by
Kota Miura
Guillaume Jacquemet
4 months ago
Also, the PDF or our preprint was created with Rχiv-Maker
@henriqueslab.bsky.social
rxiv-maker.henriqueslab.org
Paper:
arxiv.org/html/2508.00...
add a skeleton here at some point
0
11
6
reposted by
Kota Miura
EMBL
4 months ago
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-...
11
254
78
reposted by
Kota Miura
Juanma García-Arcos
4 months ago
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
6
83
34
reposted by
Kota Miura
Dave Barry
4 months ago
BIOIMAGE ANALYSTS ASSEMBLE!!!
#CBIAS2025
1
54
23
reposted by
Kota Miura
GloBIAS
4 months ago
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.
0
0
7
reposted by
Kota Miura
Elnaz
5 months ago
Opening of the networking dinner by traditional sake opening ceremony
#GloBIAS2025
#BioimageAnalysis
@kbias.bsky.social
@globias.bsky.social
1
6
1
reposted by
Kota Miura
The Francis Crick Institute
7 months ago
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...
loading . . .
CBIAS napari workshop 2025
https://www.crick.ac.uk/whats-on/cbias-napari-workshop-2025
0
23
20
reposted by
Kota Miura
BoneJ
7 months ago
🔥🔥🔥 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 🤞
0
2
3
reposted by
Kota Miura
Ryan Savill
7 months ago
(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...
loading . . .
4
63
26
reposted by
Kota Miura
Daniel Krentzel
7 months ago
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...
loading . . .
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...
https://www.nature.com/articles/s41592-025-02794-0
2
43
22
reposted by
Kota Miura
NFDI4BIOIMAGE
7 months ago
✍ 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...
0
12
5
reposted by
Kota Miura
Jean-Yves Tinevez
7 months ago
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). 👇
3
52
28
GloBIAS conference Kobe 2025, the registration for the symposium is still open, until Sept 15th!
bit.ly/GloBIAS2025-...
loading . . .
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...
https://bit.ly/GloBIAS2025-Kobe
7 months ago
1
10
7
we have been working on this for some years and finally out!
add a skeleton here at some point
7 months ago
0
0
0
reposted by
Kota Miura
Nicolas Chiaruttini
10 months ago
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...).
loading . . .
2
13
1
reposted by
Kota Miura
Simon F. Nørrelykke
9 months ago
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/
1
21
6
reposted by
Kota Miura
Saul Kato
9 months ago
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...
loading . . .
"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...
https://www.focolab.org/post/surfdist-pre-print-posted
0
4
2
reposted by
Kota Miura
Jean-Yves Tinevez
9 months ago
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...
loading . . .
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...
https://forum.image.sc/t/upcoming-breaking-changes-in-trackmate-v8/114687
0
14
6
reposted by
Kota Miura
Serdar Balci
9 months ago
Using
#QuPath
with HISTAI SPIDER Colorectal Module Repository
github.com/sbalci/spide...
Video
www.youtube.com/watch?v=8tLO...
#pathsky
#digitalpathology
#pathology
#pathologist
loading . . .
GitHub - sbalci/spider-qupath
Contribute to sbalci/spider-qupath development by creating an account on GitHub.
https://github.com/sbalci/spider-qupath
0
1
1
reposted by
Kota Miura
Fabrizio Musacchio
9 months ago
✍️ 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
#eLife
add a skeleton here at some point
3
12
4
reposted by
Kota Miura
Beth Cimini 🔬💻📊
9 months ago
@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)
loading . . .
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...
https://arxiv.org/abs/2507.06407
0
9
3
reposted by
Kota Miura
CCI Uni of Liverpool
10 months ago
It has been lovely to meet Kota
@kbias.bsky.social
after all these years!
#imageanalysis
@eurobioimaging.bsky.social
0
8
1
reposted by
Kota Miura
Journal of Cell Science
10 months ago
The application deadline for our next round of 🔬Training Grants is this Friday 6 June.
www.biologists.com/grants/jcs-f...
add a skeleton here at some point
0
4
4
reposted by
Kota Miura
the Node
10 months ago
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:
loading . . .
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
https://thenode.biologists.com/visualizing-with-vibes-potential-and-pitfalls/research/
1
26
12
reposted by
Kota Miura
Joachim Goedhart
10 months ago
I do agree. Well done!
0
1
1
reposted by
Kota Miura
FocalPlane
10 months ago
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...
loading . . .
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...
https://focalplane.biologists.com/2025/05/20/imaging4all-funding/
0
0
2
The
#quarep-limi
wg12 image & analysis publication workshop @
#ELMI2025
quite successful!
10 months ago
1
10
1
Image data & analysis publication check list team (
#quarep-limi
wg12) getting ready for the workshop this afternoon
#ELMI2025
10 months ago
0
5
0
reposted by
Kota Miura
EMBL Events
10 months ago
Day 2 at
#ELMI2025
: participants and excibitors enjoying good coffee and conversations ☕🤝
0
7
1
reposted by
Kota Miura
Gabriel Krens
10 months ago
#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/
)
0
11
6
#ELMI2025
500 participations
10 months ago
0
3
0
reposted by
Kota Miura
napari
10 months ago
Reminder: the
@globias.bsky.social
2025 symposium is happening Oct 26-31 in Kobe, Japan, and, on top of many other cool bioimage analysis events, several members of the napari core team will be leading a napari hackathon. 🧑💻👩💻👨💻 Registration deadline is Jun 15!
www.globias.org/activities/b...
loading . . .
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...
https://www.globias.org/activities/bioimage-analysis-conference-2025-in-kobe
0
6
6
reposted by
Kota Miura
Anna Klemm
11 months ago
So much looking forward to this! 🤩 We're thrilled to be running a new instance of our "Advanced Methods in Bioimage Analysis" course. It's going to be a blast! Apply by June 4th.
add a skeleton here at some point
0
11
7
I posted an announcement about the GloBIAS2025 Kobe to the
forum.image.sc
. Added some more details, a lighter version of the conference website.
#GloBIAS
forum.image.sc/t/globias-co...
loading . . .
GloBIAS Conference 2025 Kobe, registration extended!
We would like to draw your attention to the GloBIAS Bioimage Analysis Conference 2025, from Oct 26, 2025, to Oct 31, 2025, in Kobe, Japan, at the RIKEN Center for Biosystems Dynamics Research, Kobe Ca...
https://forum.image.sc/t/globias-conference-2025-kobe-registration-extended/112653
10 months ago
0
1
3
A great work: A part of my PhD study was confirmed.
journals.plos.org/plosone/arti...
loading . . .
Continuous emergence of phototaxis in Dictyostelium discoideum
The evolutionary transition from uni- to multicellularity is associated with new properties resulting from collective cell behavior. The social amoeba Dictyostelium discoideum alternating between indi...
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0321614
10 months ago
1
2
0
reposted by
Kota Miura
Zac Swider
11 months ago
Just pushed v0.3.0 which builds in the lovely suite of LUTs created by
@jamesdmanton.bsky.social
also installable directly into FIJI at
sites.imagej.net/JDM_LUTs/luts/
add a skeleton here at some point
0
4
3
reposted by
Kota Miura
VIB Training & Conferences
11 months ago
Turn images into insights! Join VIB's imaging workshops in Antwerp: 🔬🖥️ Fiji Image Processing (18/06): Build your first analysis pipeline 🔬🖥️
#QuPath
Bioimage Analysis (19/06): Segment, classify & script your images For life scientists ready to level up. Details 👉
vibbio.tech/43sI2fp
#bioimaging
0
1
1
The guru's talk...
#GloBIAS
add a skeleton here at some point
10 months ago
0
0
0
Load more
feeds!
log in