Kota Miura
@kbias.bsky.social
๐ค 185
๐ฅ 113
๐ 1354
bioimage analysis, NEUBIAS, GloBIAS
https://www.globias.org/
pinned post!
what is GloBIAS? here you go...
www.youtube.com/watch?v=LPJE...
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GloBIAS: Global BioImage Analysts' society - the idea
YouTube video by GloBIAS
https://www.youtube.com/watch?v=LPJEh9qT76g
11 months ago
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Kota Miura
Ricardo Henriques
8 days ago
๐๐ฐ 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
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Kota Miura
Denis Wirtz
8 days 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.
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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
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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
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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
6 days ago
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Kota Miura
Guillaume Jacquemet
about 1 month ago
Also, the PDF or our preprint was created with Rฯiv-Maker
@henriqueslab.bsky.social
rxiv-maker.henriqueslab.org
Paper:
arxiv.org/html/2508.00...
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Kota Miura
EMBL
about 1 month ago
Anthony A. Hyman will become EMBLโs 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-...
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Kota Miura
Juanma Garcรญa-Arcos
about 1 month 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
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Kota Miura
Dave Barry
about 1 month ago
BIOIMAGE ANALYSTS ASSEMBLE!!!
#CBIAS2025
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Kota Miura
GloBIAS
about 1 month 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.
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Kota Miura
Elnaz
about 2 months ago
Opening of the networking dinner by traditional sake opening ceremony
#GloBIAS2025
#BioimageAnalysis
@kbias.bsky.social
@globias.bsky.social
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Kota Miura
The Francis Crick Institute
4 months ago
Want to enhance your image analysis skills with napari? Weโre running a two-day training event on how to use napari to effectively analyse your bioimaging data. ๐ Applications close on 15 September. Learn more and apply ๐
www.crick.ac.uk/whats-on/cbi...
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CBIAS napari workshop 2025
https://www.crick.ac.uk/whats-on/cbias-napari-workshop-2025
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Kota Miura
BoneJ
4 months ago
๐ฅ๐ฅ๐ฅ 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 ๐ค
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Kota Miura
Ryan Savill
4 months ago
(1/14) Iโm happy and proud to introduce: SpinePy โ 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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Kota Miura
Daniel Krentzel
4 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 yourself๐งต(1/9)
www.nature.com/articles/s41...
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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
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Kota Miura
NFDI4BIOIMAGE
4 months ago
โ If you're having difficulty writing
#BioimageAnalysis
code that enables others to follow your workflow, have a look at @haesleinhuepf.bsky.socials slides on โReproducible Bio-Image Analysis using Python, Napari, Jupyter and AIโ from the
#EMBOlsm25
. To the slides: ๐
doi.org/10.5281/zeno...
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Kota Miura
Jean-Yves Tinevez
4 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). ๐
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GloBIAS conference Kobe 2025, the registration for the symposium is still open, until Sept 15th!
bit.ly/GloBIAS2025-...
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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
4 months ago
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we have been working on this for some years and finally out!
add a skeleton here at some point
4 months ago
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Kota Miura
Nicolas Chiaruttini
6 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...).
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Kota Miura
Simon F. Nรธrrelykke
6 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/
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Kota Miura
Saul Kato
6 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...
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"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
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Kota Miura
Jean-Yves Tinevez
6 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...
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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
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Kota Miura
Serdar Balci
6 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
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GitHub - sbalci/spider-qupath
Contribute to sbalci/spider-qupath development by creating an account on GitHub.
https://github.com/sbalci/spider-qupath
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Kota Miura
Fabrizio Musacchio
6 months ago
โ๏ธ New in #eLife: #CellSeg3D introduces #WNet3D, a self-supervised 3D #segmentation method for #microscopy data โ 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
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Kota Miura
Beth Cimini ๐ฌ๐ป๐
6 months ago
@kbias.bsky.social
,
@pmsampaio.bsky.social
,
@tischi.bsky.social
, Rocco D'Antuono, โชand
@haesleinhuepf.bsky.social
โฌ 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)
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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
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Kota Miura
CCI Uni of Liverpool
7 months ago
โชIt has been lovely to meet Kota
@kbias.bsky.social
after all these years!
#imageanalysis
@eurobioimaging.bsky.social
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Kota Miura
Journal of Cell Science
7 months ago
The application deadline for our next round of ๐ฌTraining Grants is this Friday 6 June.
www.biologists.com/grants/jcs-f...
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Kota Miura
the Node
7 months ago
When it comes to creating plots of your data, are you team 'web apps' or 'vibe coding' with genAI-based tools? ๐ In this post, Joachim Goedhart
@joachimgoedhart.bsky.social
โฌ discusses the potentials and pitfalls of both approaches in data visualization:
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Visualizing with Vibes: Potential and Pitfalls - the Node
Anyoneโregardless of coding skillsโshould 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/
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Kota Miura
Joachim Goedhart
7 months ago
I do agree. Well done!
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Kota Miura
FocalPlane
7 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...
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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/
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The
#quarep-limi
wg12 image & analysis publication workshop @
#ELMI2025
quite successful!
7 months ago
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Image data & analysis publication check list team (
#quarep-limi
wg12) getting ready for the workshop this afternoon
#ELMI2025
7 months ago
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Kota Miura
EMBL Events
7 months ago
Day 2 at
#ELMI2025
: participants and excibitors enjoying good coffee and conversations โ๐ค
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Kota Miura
Gabriel Krens
7 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/
)
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#ELMI2025
500 participations
7 months ago
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Kota Miura
napari
7 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. ๐งโ๐ป๐ฉโ๐ป๐จโ๐ป Registration deadline is Jun 15!
www.globias.org/activities/b...
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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
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Kota Miura
Anna Klemm
8 months ago
So much looking forward to this! ๐คฉ 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.
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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...
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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
7 months ago
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A great work: A part of my PhD study was confirmed.
journals.plos.org/plosone/arti...
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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
7 months ago
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Kota Miura
Zac Swider
7 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
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Kota Miura
VIB Training & Conferences
7 months ago
Turn images into insights! Join VIB's imaging workshops in Antwerp: ๐ฌ๐ฅ๏ธ Fiji Image Processing (18/06): Build your first analysis pipeline ๐ฌ๐ฅ๏ธ
#QuPath
Bioimage Analysis (19/06): Segment, classify & script your images For life scientists ready to level up. Details ๐
vibbio.tech/43sI2fp
#bioimaging
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The guru's talk...
#GloBIAS
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7 months ago
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#GloBIAS
conference 2025 Kobe, Deadline extended to June 15th! This includes the training school, two hackathons, and taggathon registration, not only the symposium (... but sorry, the travel grant for the training school has closed)
add a skeleton here at some point
7 months ago
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Kota Miura
GloBIAS
7 months ago
Next
#GloBIAS
seminar coming up. Curtis Rueden will present on 'Fiji with Python power'. To get the link please register here:
www.globias.org/activities/b...
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Kota Miura
BioImaging North America
8 months ago
#HappyFluorescenceFriday
!
#microscopycommunity
Join
@bioimagingna.bsky.social
Early Career WG for our Career Speaker Series on The BioImaging ToolBox: โPre-nalysisโ, Imaging, Analysis and Processingโ next Thursday , May 1 Learn More & Register here
buff.ly/BHGomlc
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Kota Miura
8 months ago
๐ข Learn
#QuPath
across ๐ต๐น! The 4th edition of our Intro to QuPath course is happening: ๐๏ธ May 21โ23, 2025 ๐ PPBI Nodes across Portugal ๐น Register by May 11 ๐ Info & registration: see comments
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Kota Miura
Beth Cimini ๐ฌ๐ป๐
8 months ago
Want to hear more about the history of
@cellprofiler.bsky.social
, and about what comes next? Come listen to
@gnodar.bsky.social
and I talk about it tomorrow at the
@globias.bsky.social
seminar series - 5pm CEST/11am CDT/ 8 am PDT. Register NOW (so we have time to send you the link!) at link below!
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GloBIAS seminar series
Please fill out the form if you want to register for our GloBIAS seminar series. The next sessions will be: Wednesday, 26. March 2025 4 - 5 pm CET (3 - 4 pm GMT) Thursday, 24. April 2025 5 - 6 pm CEST...
https://docs.google.com/forms/d/e/1FAIpQLSeJru9DcVQc65rzFxU7jd88q9ZfiNWl7uGQ5Dll6UepdkuR9A/viewform
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Kota Miura
napari
8 months ago
Our next Atlantic community meeting is coming up! Wed 8:30am SFO / 11:30am NYC / 5:30pm Paris. Come chat about napari 0.6.0 (due imminently! ๐ ), ask for advice, demo your cool plugin! Agenda:
hackmd.io/BXWDZ3i8Q6OA...
Zoom:
numfocus-org.zoom.us/j/8404893043...
Calendar:
napari.org/stable/commu...
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napari Americas/Africa/Europe community meetings - HackMD
https://hackmd.io/BXWDZ3i8Q6OAEASrkaSNIQ
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Kota Miura
Latin America Bioimaging (LABI)
8 months ago
๐๐ผ Attention
#LABICommunity
Tomorrow, April 23, is the last day to apply for the free online Latin American CellProfiler Workshop! A great opportunity to dive into image analysis using CellProfiler. ๐
broad.io/latam_workshop2025
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New tool: OrgaMeas
www.sciencedirect.com/science/arti...
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OrgaMeas: A pipeline that integrates all the processes of organelle image analysis
Although image analysis has emerged as a key technology in the study of organelle dynamics, the commonly used image-processing methods, such as threshโฆ
https://www.sciencedirect.com/science/article/pii/S0167488925000692
8 months ago
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Kota Miura
Beth Cimini ๐ฌ๐ป๐
9 months ago
If you train people in ImageJ, Fiji, whatever, even if it isn't your day job, please let us know, and please share this post! Thanks a ton, we really appreciate it. (2/2)
forms.gle/C8dUpg8qZkbD...
#bioimaging
#microscopy
#bioimageanalysis
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Open Source Bioimage Analysis Training Survey
We are attempting for a publication to estimate the number of biologists who have attended a tutorial or training course in open source bioimage analysis (especially user friendly tools, but anything ...
https://forms.gle/C8dUpg8qZkbDX7mDA
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