#napari — Public Fediverse posts

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

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

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

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

✍️ 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

#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

Here is an example of using #RandomForests 🌳🌳 for #PixelClassification 🖼️ in #Python 🐍, using @napari for labeling ✍️

🌎 https://www.fabriziomusacchio.com/blog/2023-06-23-_random_forests_pixel_classifier/

#RandomForest #Napari #MachineLearning #ImageProcessing #Bioimage #BioimageAnalysis

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.

#java #python #kotlin #groovy

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.

#java #python #kotlin #groovy

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.

#java #python #kotlin #groovy

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.

#java #python #kotlin #groovy

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.

#java #python #kotlin #groovy

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.
#java #python #kotlin #groovy

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.
#java #python #kotlin #groovy

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.
#java #python #kotlin #groovy

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.
#java #python #kotlin #groovy