🚨Gearing up for #NGFF 0.6! 🚨
Help us give this a final push over the finish line and join us in ironing out the last flaws on the way!
More information here 👇
forum.image.sc/t/ngff-weekl...
My talk at the #I2K 2025 conference is now available online. There are also many other great talks worth checking out.
My full talk is on their YouTube and includes a hands-on walkthrough of how to use VNC-Dist:
youtu.be/ZxngGrqAr_Y?...
Pfffffff. Chains of transformations are hard. It took me two releases to get the live deskew slider right and looking ok (hopefully) #bigvolumebrowser
New video: more examples showing deep learning segmentation failure modes—and how to detect them with Napari. I show how Napari’s layer system compares images, ground truth, and results, and how Appose enables comparison across incompatible DL packages. www.youtube.com/watch?v=c369...
Some people already combine Yolo (bounding boxes) to generate a prompt for SAM (masks) it's just a bit unwieldy to do. It is also a bit slow and a memory hog compared to methods like Cellpose that output an indexed instance map. How fast is this method? Any Fiji/Napari plugins yet to test with?
I ask a lot of questions on the Napari zulip and always get answers from the core developers right away. If you want to learn more about Napari development or have general questions about Napari check out the zulip channel napari.zulipchat.com#recent. Napari is also supported on forum.image.sc.
the napari logo (a two-lobed island) modified to look like a snowman, with Christmas (red/green) colors
We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K.
opencollective.com/napari/donate
Do you think the problem is even worse then we think because while the nonsense citations are caught, reasonable sounding fake ones won't be??
If you use linkedin connect with @sabersaharkhiz.bsky.social he is posting some interesting material.
I was invited by @focalplane.bsky.social to write a short description about it:
focalplane.biologists.com/2025/12/12/a...
Myself (Toronto) and @psobolewskiphd.bsky.social (Phillies) are huge baseball fans.... that game was... I don't even know how to explain it in terms of other sports, lol. Hope you enjoyed the rest of that game (I didn't).
That was a tough one. Did he forget how many outs there were? Looked like even after the bobble he had plenty of time to throw to first.
I was searching for a Python utility for Fourier Ring/Shell Correlation. All I got in a blue sky search were 4 small posts from @christletx.bsky.social ... all I got from chatgpt was installation instructions for non-existent libraries and github repos... anyone know a good tool for this?
📢 After #CBIAS2025, join our hands-on 2-day napari training by @crick.ac.uk @ucl.ac.uk @liverpooluni.bsky.social
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025
Episode 11 - In which @erinweisbart.bsky.social and I talk about just how much we love ilastik (@ilastik-team.bsky.social) and how it's great for so many problems! Also, that you should use a small brush.
The 1st working version of my little @napari.org plugin (napari-czitools) is almost ready.
It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read.
Still quite some things to improve ...
Cell tracking is never perfect, and it's important to understand the types of errors your solution contains.
Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...
You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.
I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8
Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...
Btw, and in the spirit of #OpenScience, all my #Napari #bioimage analysis #tutorials are freely available — from basics to #segmentation, #tracking, and #clustering. Feel free to explore and share ✌️
🌍 www.fabriziomusacchio.com/teaching/tea...
Giraffe spots would be something to measure that would be corrupted by the noise too. So would want to keep them and after restoration it would be nice to be able to count the correct number of spots, shape of spots and (importantly ) intensity of spots...
Even with the really good microsam/cellposesam generalist models, annotating specialist labels and retraining is always better.
Love to hear more about testing. I'm always skeptical when I hear "new method B" outperforms previous method "A" because it often turns out "A" was not run optimally. Seems reasonable in an unsupervised or general mode this new method could be better than generalist Stardist/Cellpose but ...
You will be missed. I really appreciated you getting the North East Bioimaging meeting organized the last couple years.
🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
We released version 1.6 of micro_sam:
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
New ‘How to’ post on FocalPlane 🔬💻
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
Need help with bioimage analysis? Contact the UK Euro-BioImaging Node to see how we can help!
www.eurobioimaging-access.eu/nodes/uk-node
Want to host your own AI models without relying on external infrastructure?
Enter BioEngine
ai4life.eurobioimaging.eu/announcing-b...
Your go-to for flexible, self-hosted bioimage analysis. Open source, scalable, and built for you!
Where did you order it? Seems like the retail price is suppose to be about $2000, however online they peaked at like $5000 a month ago, but seem to be down to $3000 now.... still way above suggested retail price.
