iiinova — where your digital self keeps evolving

Johannes Soltwedel @jo-soltwedel.bsky.social · 01/10/2026

Built in by @mazoc.bsky.social: Ever looked at a scatter plot and wondered "What's the deal with that outlier"? The clusters-plotter can center the viewer to any selected object in the viewer and give you a look at whatever is messing up your results directly. Understand your data better! 📊

040

Johannes Soltwedel @jo-soltwedel.bsky.social · 01/10/2026

In the latest version, you can filter and export your selected objects (shapes, points, labels, whatever) into a fresh layer. An easy way to clear false-positives or other noise from your data interactively! Interesting for human-in-the-loop #smartmicroscopy? 🔬

140

Johannes Soltwedel @jo-soltwedel.bsky.social · 01/10/2026

Just released the napari-clusters-plotter 0.11.0 github.com/BiAPoL/napar..., a little passion-project of mine for interactive exploration of datasets and attached features in @napari.org Two cool things to take note of 👇

github.com

GitHub - BiAPoL/napari-clusters-plotter: A napari plugin for clustering objects according to their properties.

A napari plugin for clustering objects according to their properties. - BiAPoL/napari-clusters-plotter

13113

Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026

There are other things to do with bio-images 🔬🦠🧫with this standard and I'm thrilled to see more of this data appear and more tools supporting it. Make sure to visit ngff.openmicroscopy.org @openmicroscopy.org for the latest 📜publications, ⚒️ tools and 🌍 community events (we're nice ❤️)

ngff.openmicroscopy.org

OME-Zarr — NGFF documentation

050

Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026

🤝Coordinate transformations extend the promise of interoperability to complex, non-linear transformations. Do a registration in imagej.net/plugins/bigw... @bogovicj.bsky.social in #Fiji, store the NGFF transform and apply it to your data elsewhere! (Dataset: rodare.hzdr.de/record/3131)

1102

Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026

🟦🟦🟦 Less fancy, just as handy: Attaching simple translations to your image tiles allows the #stitching tool of your choice (here: github.com/multiview-st... at work in @napari.org) and just hit "Fuse". Dataset from github.com/JaneliaSciCo...

171

Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026

OME-Zarr 0.6 allows to compose multi-modal image data across dimensionalities into a joint dataset and ingest it into a supporting viewer of your choice. Combining image data across scales from µm 🧫 to cm 🧠 and beyond will be much easier now! Dataset source: rodare.hzdr.de/record/3131

1104

Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026

The main new things in 0.6 are ✨transformations ✨ - adding the "Where" directly to your image data. Some data (e.g., SCAPE microscopy) require a transform to display correctly. View your data correctly, data-duplication free with OME-Zarr 0.6! (UI is WIP, made for @napari.org x napari-ome-zarr)

192

Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026

🚨New release: NGFF specification 0.6 🚨 Last week, we formally released the latest version of the NGFF specification: 0️⃣.6️⃣( ngff.openmicroscopy.org/specificatio...) Let's take a small tour through the things possible with #ome-zarr 0.6 now that this is out! 👇

ngff.openmicroscopy.org

Version 0.6 — NGFF documentation

12311

Reposted by Johannes Soltwedel

Claas Gefroi @claasgefroi.bsky.social · 17/09/2026

Könnte vielleicht auch daran liegen, dass es in Kanada verlässliche Rahmenbedingungen gibt, sprich: keinen russlandfreundlichen Regierungschef, kaum Rassismus und keine Rechtsextremisten ante portas.

Tweet von Michael Kretschmer:
Das Pharmaunternehmen #GlaxoSmithKline wird seine #Produktion von Dresden nach Kanada verlagern. Da müssen wir uns fragen: Was unterscheidet den Produktionsstandort von #Deutschland?

#Energie ist in Kanada deutlich günstiger als bei uns. Die Menschen arbeiten dort durchschnittlich 1.600 statt 1.300 Stunden im Jahr. Hinzu kommen bei uns immer mehr Vorgaben und #Bürokratie – von der Kommunalabwasserrichtlinie bis zur Verpackungsverordnung.

Die geplante Schließung zeigt exemplarisch die Probleme unseres Wirtschaftsstandorts. Deutschland hat es in der Hand, diese Bedingungen zu verbessern.

58705112

Reposted by Johannes Soltwedel

Juan Nunez-Iglesias @jni.codes · 20/08/2026

Me: it is perfectly safe to run this find/sed command, as I am version-controlling my files with git. Sed command: ✨ I am editing files inside .git ✨ Me: Well. Fuck.

181

Reposted by Johannes Soltwedel

ADFC Sachsen e. V. @adfcsachsen.bsky.social · 15/09/2026

Seit 25 Jahren arbeitet der #ADFC daran, dass man am Bahnhof #Dresden Neustadt sein Rad gut abstellen kann: Regengeschützt, diebstahlsicher und geschützt vor Vandalismus. Heute war erster Spatenstich! Das ist wirklich ein guter Tag für das #Fahrradland Sachsen. 💗🚲 www.diesachsen.de/dresden-news...

diesachsen.de

Ende des Park-Chaos am Bahnhof Neustadt: Neues Fahrradparkhaus kommt!

Nie wieder Angst ums teure E-Bike! Ein beleuchteter Holzbau bringt überdachte Stellplätze und ein stadtweites Buchungssystem nach Dresden.

0104

Reposted by Johannes Soltwedel

German BioImaging @gerbi-gmb.de · 28/08/2026

"What the heck is…OME-zarr/NGFF" Demystifying bioimaging tech: no jargon, no judgment, just real conversation with @jo-soltwedel.bsky.social on the latest tools & trends. 📅 Sept 3, 1–2:30 PM (Zoom) Register: t1p.de/0byxl | Infos: t1p.de/zkcnd #opensource #ngff #ome #bioimaging

0137

Johannes Soltwedel @jo-soltwedel.bsky.social · 27/08/2026

Benutze einen TSUN Wechselrichter, eine Marstek Batterie und einen semi-selbstgebauten Tasmota IR Lesekopf am Zähler. Alle davon kommunizieren über MQTT und entsprechende Integrationen mit Homeassistant und lassen sich auch steuern. Die Hersteller-Apps sind alle gelöscht 👍

010

Reposted by Johannes Soltwedel

Max Planck Institute of Molecular Cell Biology and Genetics @mpi-cbg.de · 24/08/2026

We are celebrating 25 years since opening our building in Dresden on January 22, 2001! #25yearsmpicbg www.mpi-cbg.de/news-outreac...

04012

Reposted by Johannes Soltwedel

Aafke Gros @aafkegros.bsky.social · 24/07/2026

Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...

A FIB-SEM plankton visualization where the top shows only the volumetric data of the chromosomes, and the bottom a normally sliced region of the cell.

A fluorescence microscopy dataset where a region has been reloaded to be much higher resolution

26827

Johannes Soltwedel @jo-soltwedel.bsky.social · 17/08/2026

A projectAxis is just a particular kind of transform, more or less a non-square affine. Adding or dropping dimensions just becomes a lot easier to express as opposed to wrangling affine matrices 👍

010

Johannes Soltwedel @jo-soltwedel.bsky.social · 17/08/2026

One cool feature in the latest #ome-zarr spec are "projectAxis" transforms 📽️: Projecting images into higher dims (i.e. 2D->3D) is absolutely transformative for some use cases! Now to do this with maaaany more slides 🔬 Dataset from rodare.hzdr.de/record/3131 cc @napari.org

1315

Reposted by Johannes Soltwedel

Joel Lüthi @joelluethi.bsky.social · 14/08/2026

We're excited to announce the 2026 OME-Zarr hackathon 🎉 📅 Date: November 2nd - November 6th 2026 📍 Location: University of Zurich, Zurich, Switzerland 💻 Virtual participation: possible for Monday afternoon, 1:00 PM CET 6:00 PM CET biovisioncenter.notion.site/2026-ome-zar... (1/6 🧵)

11414

Reposted by Johannes Soltwedel

Cleanthinking.de - Sauber in die Zukunft @cleanthinking.wsocial.eu · 14/08/2026

Der Basiseffekt der Erderhitzung wurde schon 1912 verstanden, wie das Bild zeigt, dass Gavin Mooney heute gepostet hat. Glückwunsch an die Menschheit für ein Jahrhundert Ignoranz.

461026381

Johannes Soltwedel @jo-soltwedel.bsky.social · 23/07/2026

Not going to be in Cracow for the big event so had to make do with a small impromptu @napari.org x @openmicroscopy.org #omezarr Hackathon in Bern 🔬🇨🇭 @m-albert.bsky.social @guiwitz.bsky.social

0162

Johannes Soltwedel @jo-soltwedel.bsky.social · 18/07/2026

Just passing through, but wouldn't miss this stunning piece of #brutalism - St. Joseph in #lehavre, France

Interior of st. Joseph in Le Havre, France

030

Reposted by Johannes Soltwedel

napari @napari.org · 12/07/2026

Struggling for something to do in a TWO DAY gap without ⚽? How about trying our pre-release of napari 0.8.0? napari.org/dev/release/... Of note, this release drops Py3.10 support and deprecates PyQt5 in favor of PyQt6. It also adds some neat new features and improvements! See below: 👇

1259

Reposted by Johannes Soltwedel

Maja Göpel @beyond-ideology.bsky.social · 07/07/2026

Warum fällt es mir schwer, hier an Zufall zu glauben? Und selbst wenn es einer sein sollte: das ist ein Versagen vermeintlich „neutraler“ KI. Gerade im Vergleich zu Claude mit viel ausgewogeneren Werten.

Tabelle, welche Nachrichtenportale von ChatGPT am meisten zitiert werden und „welt.de“ vom Springer Konzern liegt mit 264 mit sehr großem Abstand an der Spitze. Dahinter liegt Deutschlandfunk mit 55 und graduell absteigend weitere 8 Medien bis zum Wert 12.

1192219779

Johannes Soltwedel @jo-soltwedel.bsky.social · 07/07/2026

If the Imaris format is supported by Bioformats, I would try the www.glencoesoftware.com/products/ngf...? Otherwise check out ngff.openmicroscopy.org/resources/to... 👍

glencoesoftware.com

110

Johannes Soltwedel @jo-soltwedel.bsky.social · 03/07/2026

There are bound to be more 🤯-kind of use cases waiting to be implemented and published. Follow us on the image.sc dev thread forum.image.sc/t/ngff-weekl... for information about cool datasets, upcoming implementations across the @openmicroscopy.org OME-verse and get in touch 👉

forum.image.sc

NGFF weekly dev update thread

Done and dusted: 🎁 ngff specification 0.6 🥳 (rc0) Alright, everyone here it is: I just released the ngff specification 0.6(rc0) 🤔 ...Why rc0? Ultimately, we need to abide by the results and constrai...

041

Johannes Soltwedel @jo-soltwedel.bsky.social · 03/07/2026

...or image #stitching, where a microscope 🔬 could just write out multiscale tiles on-the-fly along with the coordinates of each tile in the image. An application like @napari.org can then just parse these in and forward it to tools like multiview-stitcher.github.io/napari-stitc...

120

Johannes Soltwedel @jo-soltwedel.bsky.social · 03/07/2026

Still, what's new? My personal favorite: The scene 🎥 Thanks to a now standardized set of transformations, you can write out the spatial relationships between (multi-modal) images, which is super neat in image registration... (Dataset: rodare.hzdr.de/record/3131)

182

Johannes Soltwedel @jo-soltwedel.bsky.social · 03/07/2026

First, why 0.6rc0? The door is closed for changes to the spec after we allowed ourselves some iterating (orange arrow). However: we need to give developers the time to update their implementations (green arrow) before the #NGFF RFC process allows us to hit the switch ⚡on a formal 0️⃣.6️⃣

110

Johannes Soltwedel @jo-soltwedel.bsky.social · 03/07/2026

🚨Just out: #NGFF specification 0.6 (rc0): ngff.openmicroscopy.org/specificatio... What's new, what's what? Short thread 🧵👇

ngff.openmicroscopy.org

Version 0.6rc0 — NGFF documentation

2123

Johannes Soltwedel @jo-soltwedel.bsky.social · 02/07/2026

That's one satisfying github notification list to end the day with 🏝️ Now just one more thing to do...

A github notification list with many fixed issues and merged pull requests.

151

Reposted by Johannes Soltwedel

German BioImaging @gerbi-gmb.de · 29/06/2026

🚨 TiM2027 Deadline Extended! More time to submit your workshop! New deadline: July 14, 2026 Don’t miss your chance. 🔗 Apply now #TiM2027 #DeadlineExtended #Microscopy

067

Reposted by Johannes Soltwedel

Voilà: Francis Gagnon @chezvoila.com · 25/06/2026

Nothing like a good chart comparing projections vs actuals. We need more of these! 📊

Two line charts side by side.
Left: Annual carbon storage. About 20 projection lines show optimistic scenarios with considerable growth. The line for actual capacity is pracitcally flat.

Right: Solar power. About 40 lines for projections show growth of varying degrees. The line for actual solar electricity production is much steeper than all of the projections, showing chronic underestimation.

Source: ProPublica

0224

Johannes Soltwedel @jo-soltwedel.bsky.social · 25/06/2026

Just the occasional this-thing-is-really-easy-in-ome-zarr-0.6 kind of post: Stitching in napari @napari.org with napari-stitcher (@m-albert.bsky.social) and napari-ome-zarr (@will-j-moore.bsky.social) (WIP) : (Sample data from the awesome big-stitcher tool github.com/JaneliaSciCo...)

0227

Reposted by Johannes Soltwedel

Michael Friendly @datavisfriendly.bsky.social · 25/06/2026

#TodayinHistory #dataviz #Onthisday #OTD 📊 🎂Jun 24, 1738 Johann Friedrich von Charpentier born in Dresden, Germany 🇩🇪 In 1778 he made insightful & delightful geological maps of distribution of soils, minerals 😻Gotta love that legend/palette in the detail

Detail of Charpentier's map of soils and minerals showing the color/shading legend on a pile of stone blocks

Portrait of Johann Friedrich von Charpentier

061

Reposted by Johannes Soltwedel

Parents For Future #EndFossilFuels 🪧🛢️❌ @parentsforfuture.de · 23/06/2026

Zugbetrieb Bundesweit eingestellt www.zuginfo.nrw Aufgrund eines Ausfalls des Zugfunkes ist der Zugbetrieb Bundesweit eingestellt. Das Ende können wir leider noch nicht abschätzen. Grund: Technische Störung am #Zugfunk. Sobald uns weitere Informationen vorliegen wird die Meldung aktualisiert. 😮

tagesschau.de

Nordrhein-Westfalen: Bahnverkehr bundesweit komplett eingestellt

Die Bahn hat gerade offenbar massive Probleme mit dem Zugfunk. Deshalb ist der Zugbetrieb bundesweit eingestellt worden.

4279

Reposted by Johannes Soltwedel

Zach | Last Place Comics @lastplacecomics.bsky.social · 28/05/2025

🍝 Pasta Man 🍝

638241

Reposted by Johannes Soltwedel

Chris Schmidt @handle.invalid · 19/06/2026

4 days of #ELMI2026 have just come to an end. A huge thank you and congratulations to @ppbioimaging.bsky.social for an outstanding organization and hospitality. It was an honor to participate and represent @nfdi4bioimage.bsky.social's work within this great scientific community. 👏🙏

0113

Reposted by Johannes Soltwedel

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 19/06/2026

You can't spell AI without FAIR❗ Here are the presentation slides from @jo-soltwedel.bsky.social talk, "You Can't Spell AI Without FAIR: How Data Management Leaves Footprints in Image Analysis," presented at the #ELMI2026 conference. 👉 Find the presentation on Zenodo: doi.org/10.5281/zeno...

0114

Johannes Soltwedel @jo-soltwedel.bsky.social · 17/06/2026

🚨New release 🚨 We just released ome-zarr-py 0.18 (pypi.org/project/ome-...), which brings an all new, shiny API for reading and writing #OME-ZARR data. Check out the documentation 📚 for more hints: ome-zarr.readthedocs.io/en/stable/ @openmicroscopy.org @will-j-moore.bsky.social

085

Johannes Soltwedel @jo-soltwedel.bsky.social · 16/06/2026

Great interactive talk about surveys/interactive survey about talks and cognitive biases from my colleague @lisa-schaefer.bsky.social from @gerbi-gmb.de at #ELMI2026

0143

Johannes Soltwedel @jo-soltwedel.bsky.social · 16/06/2026

Hope I didn't dig away too much of what you were planning 🫣 But repetition solidifies the message :D

110

Johannes Soltwedel @jo-soltwedel.bsky.social · 16/06/2026

Just gave a talk at #ELMI2026 and a panel discussion about how #FAIR data impacts #AI and its use in #bio-image-analysis 🔬🧪- and what we at @gerbi-gmb.de do about it 👷👷‍♀️ Slides available here: zenodo.org/records/2070...

0215

Reposted by Johannes Soltwedel

Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 17/11/2025

Turns out, there are fully opened LIDAR point scans of the whole Netherlands surface available geotiles.nl With up to 25 cm. It was hard not to load our building and around it into #bigvolumebrowser (22 M points + Fire LUT for height)

2323