#napari — Public Fediverse posts

🔬 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

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

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! 👌

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

#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

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

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

We are exceedingly pleased to announce the release of ITKElastix 0.16.0 for rigid and nonrigid registration of N-dimensional images. 🗺️🧠🙌#itk #elastix #monai @projectjupyter #napari #registration #python

https://forum.image.sc/t/itkelastix-0-16-0-has-been-released/77545

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