#napari — Public Fediverse posts

https://github.com/MercaderLabAnatomy/napari-tmidas

#BioImageAnalysis #napari

https://github.com/MercaderLabAnatomy/napari-tmidas

#BioImageAnalysis #napari

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

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

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

🔬 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

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

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.

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

✍️ 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

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

We manage to introduce a pipeline mixing spatialdata, #scPRINT #HEST1K #CONCH #SPATIALDATA and #NAPARI. Our first POC was STsimilarity: finding similar image patches across a large database of histopatologic slides.
2/6

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

#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

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

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

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

#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.

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.

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!

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

A fun napari script based on this Shadertoy: https://www.shadertoy.com/view/mtyGWy

Code here: https://gist.github.com/kephale/ae62ed52f11409e35fcba75b00992e71

Tooted from #napari with #tootapari.

@jni @SciPyConf @scipy2023 @napari
@melissawm

#napari is SO cool!!!!!

Fun with Penrose tilings in #napari. Tooted from #napari with #tootapari.

@pybonacci #napari looks worth a look, but it isn't immediately obvious that is more similar to what I'm describing than #pyqtgraph is.

I was just looking at #gamedev engines separately and thinking about how much more control of movement and viewpoint they have than plotting tools, even though in my mind "world exploration" and "data exploration" are essentially the same.

One is a physical space and the other is a parameter space.