Johannes Soltwedel
@jo-soltwedel.bsky.social
Post-doc in Bio-image analysis @PoL, TU Dresden, Physicist, Python code-jockey, train enthusiast.
Hopping on the ✨ 🚅 to Dresden after a week of #OME_NGFF_Hackathon. Looking forward till next time 😃
November 14, 2025 at 7:08 PM
Hopping on the ✨ 🚅 to Dresden after a week of #OME_NGFF_Hackathon. Looking forward till next time 😃
Happy Hackers @ #OME_NGFF_Hackathon
November 13, 2025 at 11:06 PM
Happy Hackers @ #OME_NGFF_Hackathon
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
November 12, 2025 at 5:00 PM
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
Whenever I feel down, I have a 👀 at the download statistics of that #opensource data-repository I and my team at OncoRay (Dresden) compiled during my PhD at @tudresden.bsky.social @hzdr.bsky.social.
😌
rodare.hzdr.de/record/3131
😌
rodare.hzdr.de/record/3131
August 7, 2025 at 8:54 AM
Whenever I feel down, I have a 👀 at the download statistics of that #opensource data-repository I and my team at OncoRay (Dresden) compiled during my PhD at @tudresden.bsky.social @hzdr.bsky.social.
😌
rodare.hzdr.de/record/3131
😌
rodare.hzdr.de/record/3131
Suitable @poldresden.bsky.social farewell cake for a #bioimage analyst? 🥮🤤
July 21, 2025 at 8:46 PM
Suitable @poldresden.bsky.social farewell cake for a #bioimage analyst? 🥮🤤
Broken gif in original post 😱...better look at the new feature of the @napari.org-clusters-plotter here 👇
July 16, 2025 at 8:27 PM
Broken gif in original post 😱...better look at the new feature of the @napari.org-clusters-plotter here 👇
#bioimage 🔬 data #visualization and #exploration in @napari.org with the napari-clusters-plotter (0.10.0) becoming yet a bit more versatile: Select objects & put them into new layers for processing, introspection or whatever. Works for all layers, of course! #bioimageanalysis
@mazoc.bsky.social
@mazoc.bsky.social
July 16, 2025 at 2:09 PM
#bioimage 🔬 data #visualization and #exploration in @napari.org with the napari-clusters-plotter (0.10.0) becoming yet a bit more versatile: Select objects & put them into new layers for processing, introspection or whatever. Works for all layers, of course! #bioimageanalysis
@mazoc.bsky.social
@mazoc.bsky.social
@stadt-dresden.bsky.social covered in smoke from earby wildfires. So this really is the new normal, huh...😒 #climatechange
July 3, 2025 at 11:05 AM
@stadt-dresden.bsky.social covered in smoke from earby wildfires. So this really is the new normal, huh...😒 #climatechange
Finally some feature processing: I personally find getting a feeling for some #unsupervised #ML parameters hard, e.g., in dimensionality reduction/ #clustering.
Click yourself through the parameters and see what happens interactively!
Needless to say, the algorithms are extensible⬆️📈
Click yourself through the parameters and see what happens interactively!
Needless to say, the algorithms are extensible⬆️📈
June 17, 2025 at 10:54 PM
Finally some feature processing: I personally find getting a feeling for some #unsupervised #ML parameters hard, e.g., in dimensionality reduction/ #clustering.
Click yourself through the parameters and see what happens interactively!
Needless to say, the algorithms are extensible⬆️📈
Click yourself through the parameters and see what happens interactively!
Needless to say, the algorithms are extensible⬆️📈
Shapes 📐: The new clusters-plotter automatically assigns a fitting colormap to "categorical" features, which is neat when visualizing, e.g. skan (skeleton-analysis.org) #skeletons: Skeleton ids are then automatically assigned fitting colors - no need for manual selections!
June 17, 2025 at 10:54 PM
Shapes 📐: The new clusters-plotter automatically assigns a fitting colormap to "categorical" features, which is neat when visualizing, e.g. skan (skeleton-analysis.org) #skeletons: Skeleton ids are then automatically assigned fitting colors - no need for manual selections!
With a little help from @stefanhahmann.bsky.social , tracking data is now supported, too. Goes to show the frame-highlighting for #timelapse ⌛data in the new version:
June 17, 2025 at 10:54 PM
With a little help from @stefanhahmann.bsky.social , tracking data is now supported, too. Goes to show the frame-highlighting for #timelapse ⌛data in the new version:
More supported layers: A major upgrade allows to interact with all sorts of @napari.org layer types: Labels🏷️, Points✴️, Vectors🏹, Shapes🔻, Tracks🔀 and even Surfaces⚫!
Particularly cool about Surfaces: @mazoc.bsky.social's histogram view leaves unselected areas transparent!
👉 pypi.org/project/biap...
Particularly cool about Surfaces: @mazoc.bsky.social's histogram view leaves unselected areas transparent!
👉 pypi.org/project/biap...
June 17, 2025 at 10:54 PM
More supported layers: A major upgrade allows to interact with all sorts of @napari.org layer types: Labels🏷️, Points✴️, Vectors🏹, Shapes🔻, Tracks🔀 and even Surfaces⚫!
Particularly cool about Surfaces: @mazoc.bsky.social's histogram view leaves unselected areas transparent!
👉 pypi.org/project/biap...
Particularly cool about Surfaces: @mazoc.bsky.social's histogram view leaves unselected areas transparent!
👉 pypi.org/project/biap...
FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging
Let's have a look 👇🧪💻🔬
Let's have a look 👇🧪💻🔬
June 17, 2025 at 10:54 PM
FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging
Let's have a look 👇🧪💻🔬
Let's have a look 👇🧪💻🔬
Secondly, which I think is very cool: You can now draw annotations in napari and upload them to OMERO. Hopefully this makes annotating large datasets a lot less painful! 💥
(Nevermind my shonky drawing - don't annotate like me 😄)
Looking forward to feedback/bug reports: github.com/tlambert03/n...
(Nevermind my shonky drawing - don't annotate like me 😄)
Looking forward to feedback/bug reports: github.com/tlambert03/n...
May 12, 2025 at 11:16 AM
Secondly, which I think is very cool: You can now draw annotations in napari and upload them to OMERO. Hopefully this makes annotating large datasets a lot less painful! 💥
(Nevermind my shonky drawing - don't annotate like me 😄)
Looking forward to feedback/bug reports: github.com/tlambert03/n...
(Nevermind my shonky drawing - don't annotate like me 😄)
Looking forward to feedback/bug reports: github.com/tlambert03/n...
New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
May 12, 2025 at 11:16 AM
New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
That's cool: For a brief amount of time yesterday on May 1st, #solarpower accounted for the entire entire demand of the German grid - and more! Makes me happy to contribute with my measly 800W on my balcony 😅
May 2, 2025 at 7:02 AM
That's cool: For a brief amount of time yesterday on May 1st, #solarpower accounted for the entire entire demand of the German grid - and more! Makes me happy to contribute with my measly 800W on my balcony 😅
Some new additions for the upcoming @napari.org clusters-plotter version 👉0.9.0 around the corner! Powered by some work from @mazoc.bsky.social, it casually turns into a pretty neat tool for feature map creation 😀
github.com/BiAPoL/napar...
github.com/BiAPoL/napar...
April 12, 2025 at 12:56 PM
Some new additions for the upcoming @napari.org clusters-plotter version 👉0.9.0 around the corner! Powered by some work from @mazoc.bsky.social, it casually turns into a pretty neat tool for feature map creation 😀
github.com/BiAPoL/napar...
github.com/BiAPoL/napar...
April 4, 2025 at 2:57 PM
2hrs into #TiM2025 and already mind=🤯. Rendering entire animals and human organoids in 3D and observing organism-wide disease distributions by @erturklab.bsky.social
March 17, 2025 at 2:00 PM
2hrs into #TiM2025 and already mind=🤯. Rendering entire animals and human organoids in 3D and observing organism-wide disease distributions by @erturklab.bsky.social
Fancy new #3dprinting toy 🤩 Maybe I'll start printing all my collaborators some of their data for segmentation tasks as giveaways 🤗
February 10, 2025 at 9:48 PM
Fancy new #3dprinting toy 🤩 Maybe I'll start printing all my collaborators some of their data for segmentation tasks as giveaways 🤗
Preliminary balance of my balcony #solar plant: Bought in August, produced a total of 323kWh in 2024, consumed a total of 194kWh myself. At 30ct/kWh, that's around 60€ in savings. Together with the 300€ grant from #saxony state, this should redeem itself fairly quickly :)
January 11, 2025 at 1:12 PM