@will-j-moore.bsky.social
📤 80
📥 63
📝 30
reposted by
Josh Moore
13 days ago
ICYMI (I did 🫣) 💚
add a skeleton here at some point
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2
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reposted by
Image Cooperative
13 days ago
Member Eric Perlman takes the stage at
@embl.org
to announce our launch as an international worker co-op for
#OSS
scientific imaging software. First task supported by
@biohub.org
is accelerating
#OMEZarr
towards a 1.0 alpha early 2027. Stay tuned!
image.coop
#GIDE2026
@gideproject.bsky.social
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reposted by
NFDI4BIOIMAGE
13 days ago
What's new in Ome-Zarr 0.6? Ome-Zarr is a cloud-optimised next-generation file format
#NGFF
for bioimaging, aiming to increase
#FAIR
access and remove barriers in the scientific process. The latest version offers numerous improvements and features. 👉 Find out more on Zenodo:
doi.org/10.5281/zeno...
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reposted by
OME
15 days ago
#OME2026
has come to an end—what an inspiring and collaborative few days. Huge thanks to
@nfdi4bioimage.bsky.social
for documenting the meeting so thoroughly—definitely worth a look back through their posts! But first, enjoy the wrap-up video presented already during the closing session! 🤩
add a skeleton here at some point
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reposted by
NFDI4BIOIMAGE
19 days ago
#OME2026
is coming to an end. It has been a truly welcoming, motivating, and inspiring experience full of intensive exchange and shaped by an exceptionally open and collaborative spirit. Grateful for the many insightful discussions, new connections, and shared ideas. Thank you!
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reposted by
NFDI4BIOIMAGE
20 days ago
Great talks and fruitful discussions on day 1 of the
#OME2026
Community Meeting in Düsseldorf with demonstrations of using OMERO, OME-Zarr, and other OME tools in material sciences, palynology, spatial omics and more. Now starting: The Poster session. 📜💬🗨️
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reposted by
Tiago Lubiana
20 days ago
now
@will-j-moore.bsky.social
and the new developments in ome-zarr.js
github.com/BioNGFF/ome-...
#OME2026
0
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2
reposted by
Johannes Soltwedel
21 days ago
Finally turning a lot of Github handles into real-world acquaintances and meeting many friends from the field 😀 Looking forward to three days of
@openmicroscopy.org
#OME2026
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reposted by
Josh Moore
26 days ago
Really excited to finally share this more widely. This is exactly the kind of work we hoped the cooperative could support—helping turn strong community momentum around
#OMEZarr
into something more coordinated and sustained. Very curious to hear what people think.
add a skeleton here at some point
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reposted by
Utz Ermel
28 days ago
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of
#cryoET
data! Whether you're picking particles or curating segmentations, copick reduces friction and brings
#OME-Zarr
to cryoET without breaking pipelines. 🧵👇
doi.org/10.1002/pro.70578
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Looking forward to our workshop "OMERO.figure embraces OME-Zarr" at
#OME2026
in just over a week. You can just have a go with the app at
ome.github.io/omero-figure/
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OMERO.figure
https://ome.github.io/omero-figure/
about 1 month ago
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reposted by
Martin Panknin
about 2 months ago
Kiln also has experimental OME-Zarr support. This is the Beechnut — a 3 GB micro-CT scan streamed directly from a public OME-Zarr store into the browser. No preprocessing, no conversion.
github.com/MPanknin/kil...
#WebGPU
#OMEZarr
#VolumeRendering
0
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reposted by
Juan Nunez-Iglesias
2 months ago
So… um… 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! ❤️🔥 Read the linked post for the lowdown.
add a skeleton here at some point
0
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reposted by
Image Cooperative
2 months 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...
8
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reposted by
Johannes Soltwedel
2 months 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! 🤯
add a skeleton here at some point
0
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1
reposted by
Joel Lüthi
2 months ago
We’re 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 / 10🧵)
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
2 months 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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15
5
reposted by
Ulrike Boehm
3 months ago
𝗘𝘅𝗰𝗶𝘁𝗶𝗻𝗴 𝗗𝗲𝘃𝗲𝗹𝗼𝗽𝗺𝗲𝗻𝘁𝘀 𝗶𝗻 𝗠𝗶𝗰𝗿𝗼𝘀𝗰𝗼𝗽𝘆 𝗥𝗲𝗽𝗼𝗿𝘁𝗶𝗻𝗴! 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
🔗
rupress.org/jcb/article/...
0
19
14
reposted by
OME
3 months 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/
1
16
6
reposted by
NFDI4BIOIMAGE
3 months 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). 👉 Find out more about the workflow:
zenodo.org/records/1845...
0
7
2
reposted by
Talley Lambert
3 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.
5
39
10
reposted by
Philippe Bastin's Lab
4 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
6
reposted by
German BioImaging
4 months ago
Great news for German
#BioImaging
! 🤝
#GerBI
&
#de.NBI
just signed an MoU to launch a GerBI
#OMERO
platform. de.NBI brings the cloud, GerBI handles ops, support & community. 🧩 A testbed + training hub for everyone. Stronger data, stronger science. More soon!
0
10
3
reposted by
German BioImaging
4 months ago
19th
#OME
Community Meeting, Düsseldorf · 28–30 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 Universität Düsseldorf. Invited Speakers Carole Goble – Keynote – Jean-Marie Burel Josh Moo...
https://gerbi-gmb.de/event/ome-2026-community-meeting/
0
9
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reposted by
Lucien Hinderling
4 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
4 months ago
Kind of flew under the radar, BUT we released napari-omero 0.6 recently 🥳
@openmicroscopy.org
You can now down-/upload ROIs from and to OMERO inside
@napari.org
🤩Bringing 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: Rémy 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
4 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
5 months ago
0
1
0
reposted by
5 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 🙃, 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
5 months ago
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking. It’s 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
6 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 🇺🇦
6 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, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s 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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35
reposted by
Virginie Uhlmann
6 months ago
So nice to see this!!!
add a skeleton here at some point
0
3
1
reposted by
Jacob Tomlinson
6 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 don’t hear much ab...
https://jacobtomlinson.dev/posts/2025/python-package-managers-uv-vs-pixi/
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reposted by
Johannes Soltwedel
6 months ago
This is what hacking *actually* looks like.
#OME_NGFF_Hackathon
0
17
5
reposted by
Joel Lüthi
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
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reposted by
Erick Ratamero
6 months ago
Been busy in Zürich für 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
6 months ago
0
0
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Some great talks on the first day of the
#NGFF
symposium in Zurich yesterday, including this lovely slide from Matthew Hartley,
#ome-zarr
6 months ago
0
3
0
reposted by
David Stansby
7 months ago
Today I'm announcing a new digital textbook 📖🖥️, "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
7 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 – quantixed
https://quantixed.org/2025/11/04/adventures-in-code-vii-getting-started-with-napari/
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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...
7 months ago
0
6
2
reposted by
Earthmover
7 months ago
Today, napari users can’t fully leverage Xarray’s labeled metadata, as slider names, units & dimensions often get out of sync. That’s 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
7 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
7 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
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reposted by
David Stansby
7 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. 🟥 ➡️ 🌎
add a skeleton here at some point
0
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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
7 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!
7 months ago
0
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reposted by
Stephan Preibisch
7 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 👍 for
#OME-Zarr
RFC-5. I also want to try out marimo and Web Assembly 😍
add a skeleton here at some point
7 months ago
1
3
0
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