@will-j-moore.bsky.social
๐ค 77
๐ฅ 62
๐ 29
reposted by
Juan Nunez-Iglesias
11 days ago
Soโฆ umโฆ I (and Draga Doncila Pop and Eric Perlman and
@joshmoore.bsky.social
and
@kevinyamauchi.bsky.social
) started a thing! We are excited and terrified in equal measures, and look forward to working with you all in our amazing scientific imaging community! โค๏ธโ๐ฅ Read the linked post for the lowdown.
add a skeleton here at some point
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reposted by
Image Cooperative
11 days ago
Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software.
image.coop/blog/posts/2...
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reposted by
Johannes Soltwedel
15 days ago
I'm a simple man. I see lazy streaming of chunked bio-image data from a remote
@openmicroscopy.org
#ome-zarr
image to a virtual reality
#VR
framework, I repost. Seriously, this is *so* cool! ๐คฏ
add a skeleton here at some point
0
7
1
reposted by
Joel Lรผthi
17 days ago
Weโre excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows. Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis. (1 / 10๐งต)
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.03.05.709921v1
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reposted by
Robert Haase
20 days ago
I had a great time at Uni Copenhagen giving a talk about How Generative AI impacts Bio-Image Data Science this week. You find my slides online and a recording will be shared soon!
doi.org/10.5281/zeno...
Big thanks to
@danishbioimaging.bsky.social
,
@claraprats.bsky.social
and team for hosting me!
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5
reposted by
Ulrike Boehm
25 days ago
๐๐ ๐ฐ๐ถ๐๐ถ๐ป๐ด ๐๐ฒ๐๐ฒ๐น๐ผ๐ฝ๐บ๐ฒ๐ป๐๐ ๐ถ๐ป ๐ ๐ถ๐ฐ๐ฟ๐ผ๐๐ฐ๐ผ๐ฝ๐ ๐ฅ๐ฒ๐ฝ๐ผ๐ฟ๐๐ถ๐ป๐ด! If you're involved in creating, processing, or publishing microscopy data, take a look at the new checklist for reporting requirements provided by
@quarep-limi.bsky.social
in
@jcb.org
๐
rupress.org/jcb/article/...
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reposted by
OME
29 days ago
We have integrated the Allen Institute's BioFile Finder app with IDR. You can quickly Group and Filter all images in a study. Data is served by the IDR search engine and supports up to a million images at a time. BioFile Finder links are on each study page e.g.
idr.openmicroscopy.org/study/idr0056/
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16
6
reposted by
NFDI4BIOIMAGE
about 1 month ago
Mohsen Ahmadi presents his poster, "FAIR bioimaging data management workflow for plasma medicine by integrating
#OMERO
, eLabFTW, and Adamant via
#Jupyter
notebook," at the annual meeting of the
@researchdataall.bsky.social
(#rdade2026). ๐ Find out more about the workflow:
zenodo.org/records/1845...
0
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2
reposted by
Talley Lambert
about 2 months ago
One of the funniest conversations I've ever had with Claude... stick with it through the third image to watch it slowly realize it's broken, try to "play it cool", fail spectacularly, then attempt self-aware commentary and immediately faceplant again. it's worth it, I promise.
6
29
5
reposted by
Philippe Bastin's Lab
about 2 months ago
Very emotional symposium in memory of our dear Spencer Shorte
@pasteur.fr
His legacy will be with us for ever, many thanks to Nathalie Aulner and all speakers
@krogersiooi.bsky.social
@freddyfrischknecht.bsky.social
@jytinevez.bsky.social
@yarareis-gbi.bsky.social
@stratocore.bsky.social
1
29
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reposted by
German BioImaging
2 months ago
Great news for German
#BioImaging
! ๐ค
#GerBI
&
#de.NBI
just signed an MoU to launch a GerBI
#OMERO
platform. de.NBI brings the cloud, GerBI handles ops, support & community. ๐งฉ A testbed + training hub for everyone. Stronger data, stronger science. More soon!
0
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reposted by
German BioImaging
2 months ago
19th
#OME
Community Meeting, Dรผsseldorf ยท 28โ30 April 2026 Registration is now open! Join researchers, developers, and imaging facility staff to connect, share experiences, and discuss the future of OME tools. Details & registration (deadline: 31 March 2026):
gerbi-gmb.de/event/ome-20...
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19th OME Community Meeting - German BioImaging
Join us for the 19th Open Microscopy Environment (OME) Community Meeting from 28.-30.4.2026, in the Haus der Universitรคt Dรผsseldorf. Invited Speakers Carole Goble โ Keynote โ Jean-Marie Burel Josh Moo...
https://gerbi-gmb.de/event/ome-2026-community-meeting/
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reposted by
Lucien Hinderling
3 months ago
Won best thesis award with this video! 4 years of research and play in 3 minutes :')
youtu.be/so0fPlK1-LM
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Smart microscopy, computer vision, and controlling cells with light -- my PhD thesis in 3 minutes
YouTube video by Pertz Lab
https://youtu.be/so0fPlK1-LM
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25
reposted by
Johannes Soltwedel
3 months ago
Kind of flew under the radar, BUT we released napari-omero 0.6 recently ๐ฅณ
@openmicroscopy.org
You can now down-/upload ROIs from and to OMERO inside
@napari.org
๐คฉBringing the power of napari for annotation to the management of OMERO :) Thanks
@psobolewskiphd.bsky.social
and other maintainers!
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25
11
Very pleased to announce the release of
#OMERO.figure
7.3.0 including ROI Labels, Colorbars and lots of bug fixes. Thanks to contributors: Rรฉmy Dornier,
@tom-bssnnt.bsky.social
, Jens Wendt, Niraj Kandpal.
www.youtube.com/watch?v=cUy5...
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OMERO.figure: ROI Labels and Colorbars: New in 7.3.0
YouTube video by Open Microscopy Environment
https://www.youtube.com/watch?v=cUy5NMGrlIY
3 months ago
1
3
1
As I prepare the next
#OMERO.figure
release (apologies, it's been a while) I found a video for the last release that I never published!
youtu.be/Jj-XjIhaQF4
shows Interactive Inset panels, borders, Hilo LUTs, label re-ordering etc.
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OMERO.figure new features in 2024
YouTube video by Open Microscopy Environment
https://youtu.be/Jj-XjIhaQF4
3 months ago
0
1
0
reposted by
3 months ago
#Mastodon
, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To
#cite
or not to cite shall no longer be the question ๐, because the
#preprint
. Software is available in every
#Fiji
near you.
www.biorxiv.org/content/10.6...
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49
reposted by
Zimeng Wu
4 months ago
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (โdiss trackโ) - Dynamic Sample Tracking. Itโs a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems. Preprint:
www.biorxiv.org/content/10.6...
[1/6]
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31
reposted by
OME
4 months ago
Idr0168: Prediction of protein subcellular localization in single cells from
www.nature.com/articles/s41...
by Zhang et al. Images in idr0168 are OME-Zarrs converted by the submitter.
idr.openmicroscopy.org/search/?quer...
1
0
1
reposted by
Eugene Katrukha ๐บ๐ฆ
4 months ago
Finally, the first public release of
#BigVolumeBrowser
, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
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BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, Iโd like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). Itโs a first initial public release, so there is still space for improvements. Le...
https://forum.image.sc/t/bigvolumebrowser-a-new-3d-multi-volume-mesh-point-clould-smlm-data-viewer/117764
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reposted by
Virginie Uhlmann
4 months ago
So nice to see this!!!
add a skeleton here at some point
0
3
1
reposted by
Jacob Tomlinson
4 months ago
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing. I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
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Python package managers: uv vs pixi?
When I talk to people about Python package management in 2025 I see the following tools in active use; uv, pixi, pip, conda, mamba, micromamba and poetry. There may be others, but I donโt hear much ab...
https://jacobtomlinson.dev/posts/2025/python-package-managers-uv-vs-pixi/
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reposted by
Johannes Soltwedel
5 months ago
This is what hacking *actually* looks like.
#OME_NGFF_Hackathon
0
17
5
reposted by
Joel Lรผthi
over 1 year ago
This week, we're hosting the
#OME_NGFF_Hackathon
2024 at the BioVisionCenter at the University of Zurich. We're bringing together 40 motivated researchers and specialist for
#OMEZarr
workflows,
#OMEZarr
Python tools &
#OMEZarr
Java tools. (1/3)
1
40
16
reposted by
Erick Ratamero
5 months ago
Been busy in Zรผrich fรผr the last 24h or so. Talks have been great so far, and I have a talk too. Still find it weird to see my name on a poster.
0
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Morning run to explore Zurich and grab breakfast
5 months ago
0
0
0
Some great talks on the first day of the
#NGFF
symposium in Zurich yesterday, including this lovely slide from Matthew Hartley,
#ome-zarr
5 months ago
0
3
0
reposted by
David Stansby
5 months ago
Today I'm announcing a new digital textbook ๐๐ฅ๏ธ, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
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An Introduction to OME-Zarr for Big Bioimaging Data
https://ome-zarr-book.readthedocs.io/
2
30
16
reposted by
Stephen Royle
5 months ago
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
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Adventures in Code VII: getting started with napari โ quantixed
https://quantixed.org/2025/11/04/adventures-in-code-vii-getting-started-with-napari/
3
39
16
Another
#OME-Zarr
RFC, another implementation! Started a basic display of OME-Zarr Collections (RFC-8) in ome-ngff-validator at
github.com/ome/ome-ngff...
5 months ago
0
6
2
reposted by
Earthmover
5 months ago
Today, napari users canโt fully leverage Xarrayโs labeled metadata, as slider names, units & dimensions often get out of sync. Thatโs changing. At SciPy 2025, napari, Xarray & CellProfiler devs began a collab to build true metadata-aware visualization across sciences.
earthmover.io/blog/scienti...
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Scientific Data Visualization with Xarray and Napari - Earthmover
Ian Hunt-Isaak Xarray Community Developer Tim Monko Neuroscience PhD & napari community manager This blog was also published on the xarray blog and the napari blog. TL;DR Making Napari and Xarray work...
https://earthmover.io/blog/scientific-data-visualization-with-xarray-and-napari
0
3
3
reposted by
DrLachie
5 months ago
The comedy Wildlife photography competition come at the perfect time each year
www.comedywildlifephoto.com/gallery/fina...
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These images are for viewing only and must not be copied :: Comedy Wildlife Photography Awards - Conservation through Competition
https://www.comedywildlifephoto.com/gallery/finalists/2025_finalists.php
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5
2
reposted by
Erick Ratamero
5 months ago
If you've ever worked with OME things, it is worth reading this update from Jason Swedlow on
image.sc
about the evolving OME governance. The TL;DR is that an interim leadership team has been assembled and new governance structures are coming sooner rather than later.
forum.image.sc/t/ome-transi...
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OME Transition-- Update
Dear All- Over the past two decades, OME has grown into a vibrant and global community dedicated to developing open standards, tools, and resources for the management, sharing, and analysis of micros...
https://forum.image.sc/t/ome-transition-update/117191
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14
7
reposted by
David Stansby
5 months ago
Over at `ome-zarr-models` we're working on implementing support for the new coordinate systems too - here's an example of a transformation graph from multiple tiled images that can be transformed into a common "world" coordinate system. ๐ฅ โก๏ธ ๐
add a skeleton here at some point
0
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3
Those sample datasets are public, so you can try them yourselfs. Links can also be found at
github.com/ome/ome-ngff...
add a skeleton here at some point
5 months ago
0
1
0
The
#OME-Zarr
RFC-5 proposal allows you to transform multiple images into the same coordinateSystem. Trying this out with napari at
github.com/will-moore/n...
. Cool that you can offset T-dimension as well as XYZ!
5 months ago
0
27
10
reposted by
Stephan Preibisch
6 months ago
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses.
@hhmijanelia.bsky.social
www.biorxiv.org/content/10.1...
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Very nice! Your Affine Transform blog post is really neat and just what I needed right now ๐ for
#OME-Zarr
RFC-5. I also want to try out marimo and Web Assembly ๐
add a skeleton here at some point
6 months ago
1
3
0
reposted by
Ignacio Arganda-Carreras
6 months ago
Day 5๏ธโฃ of our
@embo.org
course on "Advanced methods in bioimage analysis"! ๐ฌ๐ฅ๏ธ๐
@embl.org
@tischi.bsky.social
is already launching ๐ Lecture 4: Introduction to working with OME-Zarr (Tutorial)
@openmicroscopy.org
@zarr.dev
1
30
8
reposted by
Joel Lรผthi
6 months ago
Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr:
forms.gle/849cf2fBk1pJ...
add a skeleton here at some point
0
11
11
reposted by
Sofya Garushyants
6 months ago
hey bluesky ๐ visa hurdles mean Iโm looking for opportunities outside the US. Iโm a computational biologist (bacterial + phage genomics, postdoc in Kooninโs group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
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reposted by
NFDI4BIOIMAGE
6 months ago
What to do if you have extraordinary size data but no extraordinary local memory? ๐ฑ At the
@grcib2025.bsky.social
,
@joshmoore.bsky.social
addressed this issue in the talk โWhen Data Doesnโt Fit โ A Bioimaging Story from Files to FAIRโ. ๐ Interested?
zenodo.org/records/1708...
1
14
4
reposted by
7 months ago
Honoured to be featured - and even prouder of what the
@bioimagearchive.bsky.social
team is building together for the life sciences community.
add a skeleton here at some point
0
5
4
From
#ome-ngff-validator
you can open open
#OME-Zarr
images in a bunch of viewers, and neuroglancer's rendering of multi-channel images just got a lot nicer:
ome.github.io/ome-ngff-val...
- See
github.com/google/neuro...
7 months ago
0
15
4
reposted by
Erick Ratamero
7 months ago
new blog post: in which I talk (briefly) about getting a new job and moving back to Europe, getting a VPS, and self-hosting my code and my personal website.
pages.erickratamero.com/personal-web...
2
8
5
reposted by
Joel Lรผthi
7 months ago
You are an OME-Zarr developer yourself? Join us at the hackathon! Help push OME-Zarr towards 1.0, work on RFCs to the spec, contribute to tooling in Java or Python or build workflows using OME-Zarrs. Find out more & apply to the hackathon here:
biovisioncenter.notion.site/2025-OME-NGF...
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2025 OME-NGFF Workflows Hackathon | Notion
Date: November 12th - 14th, 2025
https://biovisioncenter.notion.site/2025-OME-NGFF-Workflows-Hackathon-25662fc04eb38148885ec0fee3ff8539?pvs=74
0
4
2
reposted by
Silvia Barbiero
7 months ago
Weโre excited to share that ez_zarr now supports Zarr v3! ๐ Huge thanks to
@mbstadler.bsky.social
&
@csoneson.bsky.social
who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting ๐ ๐
joss.theoj.org/papers/10.2110โฆ
(1/3)
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ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets
Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882
https://joss.theoj.org/papers/10.21105/joss.07882
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Currently working on
#OMERO
web-based import of public
#OME-Zarr
images
github.com/ome/omero-we...
7 months ago
0
3
1
reposted by
NFDI4BIOIMAGE
7 months ago
Poster Session at
#CoRDI2025
. Here is
@joshmoore.bsky.social
presenting how cloud-ready next-generation file formats like
#OME-Zarr
enable federated repositories with large N-dimensional arrays at peta-scale.
#OME-NGFF
@nfdi4bioimage.bsky.social
Find the poster on C.A.R.L level 2
@rwth.bsky.social
0
9
3
reposted by
Loรฏc A. Royer ๐ป๐ฌ๐งช
7 months ago
๐งฌ๐ฌ๐งช ๐ Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! ๐ฆ Ultrack โ robust, scalable nD cell tracking ๐ inTRACKtive โ a beautiful, open-source web viewer for lineage exploration Letโs dive in! ๐
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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