#napari — Public Fediverse posts

#OMIO is now at version v0.2.4. This maintenance release brings cleaner API docs, disk-backed empty image creation, and a more convenient #napari opener with automatic layer names, custom channel labels, and configurable blending ✌️

🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-4
📚 https://omio.readthedocs.io/en/latest/usage_template_functions.html#creating-empty-images-as-on-disk-zarr-arrays
📚 https://omio.readthedocs.io/en/latest/usage_core_functions.html#opening-images-in-napari-and-metadata-modification

#bioimageanalysis #Neuroscience

We are happy to announce the "NL-BioImaging Advanced Image Analysis course for biologists", 21–24 September at Erasmus MC in Rotterdam.

More info and register here:
https://courses.microscopie.nl/?event_id=527

Four hands-on days going from segmentation to full pipelines:
- Automate reproducible image processing with Jupyter notebooks
- Assess classical and AI approaches for specific challenges
- Train and optimise deep learning models on biological datasets
- Document and publish reproducible image analysis pipelines

Guidance from experts across the Netherlands.
Limited to 20 participants.

Feel free to tag colleagues or share this with your network!

#bioimaging #imageanalysis #course #openscience
#cellpose #OMERO #Jupyter #napari #FAIRdata
NL-Bioimaging #NVvM

Napari (Napal) (Navarra)
Escalada
https://montanaregulada.org/area/napari-napal?6a3a6f67b8cbe

Consulta las regulaciones actualizadas que afectan a las zonas de montaña en España.
#Escalada #montañaRegulada #Napari(Napal)

For large microscopy datasets (e.g. >1 GB): #OMIO can materialize images directly as disk-backed #Zarr stores. This allows #MemoryMapped, slice-wise access w/o loading the entire dataset into RAM. And: It fully integrates with #Napari workflows ✌️

🧵4/8

🎉 Announcing the naPLari hackathon in Kraków, Poland 🇵🇱, July 24–29 2026, after EuroSciPy!

Hack on napari, join deep dives, meet the team. All experience levels welcome!

📝 Register by July 1: napari.typeform.com/naplari-hack

#napari #ScientificPython #OpenSource #EuroSciPy #BioImageAnalysis

1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant! Use it for interactive image processing, analysis, and visualisation! Really cool project from @[email protected] from my team! #napari #bioimageanalysis #MCP @biohub

🔬 Registration is open for our pilot Introduction to napari Workshop!

napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast.

✅ Only $20 USD
✅ Limited to 20 people
✅ Perfect for biologists, imaging specialists & data scientists

Two workshops at two different times.

#napari #Python #ImageAnalysis #DataScience #OpenSource

Bioimage Analysis course at Pasteur in Paris, by Jean-Yves Tinevez and Jean-christophe Olivo-Marin.

Dates: June 1st-5th, 2026.

Deadline for application: March 1st, 2026.

With two tracks:

* ‘early career investigators track’: aims at mastering the most recent and common image analysis software tools.

* ‘analysts track’: focuses on the use of advanced algorithms and computing resources for bioimage analysis.

https://www.pasteur.fr/en/education/programs-and-courses/pasteur-courses?id_cours=32719

#ImageProcessing #BioimageInformatics #Fiji #Icy #QuPath #Napari #Ilastik #TrackMate

11/ 🔬🧪 Try it today! pip install napari-chatgpt — GitHub: github.com/royerlab/napari-chatgpt — Paper: doi.org/10.1038/s41592-024-02310-w #Omega #napari #AI #BioImageAnalysis

GitHub - royerlab/napari-chatg...

Adventures in Code VII: getting started with napari

https://quantixed.org/2025/11/04/adventures-in-code-vii-getting-started-with-napari/

#AdventuresInCode #computing #code #microscopy #napari #python

From @nvladimus : "We have opened the #mesoSPIM official User Forum" at https://forum.image.sc/tag/mesospim alongside #Fiji #ImageJ #ilastik #BiaPy #napari #DeepLabCut and many other open source softwares for bioimage informatics.

To wrap this up: Both tools are easy to test. I highly recommend trying them on your own data to see what works best for your use case.

I’ll include #CellSeg3D in our next #Napari #bioimage analysis course (https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/). Curious what impressions and feedback the students will share. 🧪🔍

What I really like about @napari is how well it integrates modern #Python tools. Great to have such a flexible, evolving #opensource platform for (bio) #imageanalysis! 👌

✍️ New in #eLife: #CellSeg3D introduces #WNet3D, a self-supervised 3D #segmentation method for #microscopy data — no labels needed. Claims to outperform #Cellpose/#StarDist on 4 datasets. Includes #opensource plugin (#Napari) + full 3D annotated #cortex dataset. Will test it later.

🌍 https://elifesciences.org/articles/99848

#DeepLearning #Neuroscience

Image analysts: What is your go to method for batch converting image files from the proprietary format to a tiff file? If this should be done at all...

I’ve been using FIJI to open and re-save mine. Although this gives me another look at the image as a QC step, I am using Napari more and more and have found a tiff easier to load into Python.

#Microscopy #ImageAnalysis #Napari #FIJI

Glad to join the Crick Bioimage Analysis Symposium for the second time (first in person!). Looking forward to two days of cool science, analyses, and technologies! @thecrick

#CBIAS2024 #ImageAnalysis #Bioinformatics #napari #pathology #pathomics

#OpenSIMMO: A fully-automated #OpenSource multicolour structured illumination module for #SuperResolution #microscopy:

-#fluorescence #microscope add-on
-#RasPi/#ESP32 control

Preprint: https://doi.org/10.1101/2024.07.04.601961
Web: https://opensimmo.github.io/
#DIYbio #lab #instruments #SIM #imaging #laser #optics #Napari #Python #ImSwitch #DMD #OpenUC2

it took longer than i care to admit to revisit Talley Lambert's revised pattern for the Pulser's library: https://github.com/kephale/pulser/blob/main/example.py

but i finally have a significant need to use this for a bespoke annotation tool. such an easy pattern to extend.

#python #midi #hci #napari

Interesting new #preprint about #tissueclearing and #lightsheet #microscopy in mouse ovaries. Complete with #napari-based deep-learning pipeline and detailed build instructions for 3D-printed sample chambers for solvent-cleared samples, so they can be viewed under a #confocal!

OoCount: A machine-learning based approach to mouse ovarian follicle counting and classification
Folts et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.05.13.593993v1

Preprint describing Nellie, a napari plugin for automated organelle segmentation. Results look impressive!

https://arxiv.org/abs/2403.13214

repo (with video): https://github.com/aelefebv/nellie

#CellBiology #microscopy #napari

#PyTME: A fast, flexible & multi-purpose template matching library for #cryoEM data:

-#OpenSource
-HT mining of cryoEM & ET datasets
-multi #CPU/#GPU support
-#Napari plugin

https://doi.org/10.1016/j.softx.2024.101636
#CompChem #bioinformatics #DIYbio #lab #instruments #microscopy #imaging #Python

Inspired by https://twitter.com/hisadan/status/1699354785441571323?s=20.
Tooted from #napari with #tootapari.

Playing with an adaptation of the processing code here (https://twitter.com/hisadan/status/1697878658437054785?s=20) to napari.
Tooted from #napari with #tootapari.

I livestreamed these blobs here: https://mastodon.social/@couldabeensci[email protected]. The #napari hackathon is done and was a success!