Working on some content for an upcoming yt-napari video tutorial and I can't resist uploading a teaser... A big part of the current yt-napari work has been connecting to other napari plugins. Here's a demo showing napari-plot-profile in action with data from yt-napari: https://youtu.be/UgNaqbtNJh0

#napari #yt #yt_astro #astrophysics #data_viz @napari

I added a new subsection to the #imageregistration chapter, demonstrating how to manually align two 3D (or 2D) stacks using @haesleinhuepf’s grandiose #Napari Assistant 🤘

🌍 https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/10_napari_image_registration#manual-image-registration

using some experimental @napari features to load in #yt AMR data on the fly:

https://youtu.be/ofoURuz-Cbw

a bit of lag, but the fact that this works at all is blowing my mind.

The dataset here is one of yt's test datasets, DeeplyNestedZoom, a cosmology simulation with 40 levels of grid refinement.

#DataVisualization #napari #OpenSource #3D #astrophysics

headed home from #scipy2023 a little early... getting ready for the flight...

fork ya?

#napari #iCanHazGenerativeYtPlot?

We've just finished our course on #Bioimage Analysis with #Napari 🧠🔬, which focusses on the practical application of @napari 🩻🔧. The course material is freely available on my website. Feel free to use and share it! 😙 #OpenScience #ImageAnalysis

🌎 https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/

As someone who doesn't do much frontend development, i'm pretty excited that i was able to refactor the #yt_napari dock widget to dynamically add/remove collapsible sections. Still gotta fix that load button since I re-wrote a bunch of the backend loading recently, but that's just a few more beeps and boops. v0.2.0, we're almost therrrrre.

#napari #yt #QT #pyqt #ICanHazFullStack

New video tutorials for the #yt-#napari plugin!

1. Intro to napari for yt users https://youtu.be/tNdIetamf98
2. Tour of the yt-napari plugin https://youtu.be/ta7rBOYNpmg

Future videos will cover more advanced usage (playlist here: https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1 )

I'll also be hosting some yt-napari live events (help & discussion sessions, more...)! Join the yt slack here https://yt-project.org/community.html and be sure to add yourself to the yt-napari channel for information.

Eric Upschulte, Forschungszentrum Jülich: Cell Segmentation with Uncertainty-Aware Contour Proposal Networks

UA-CPN to segment (natural 😜) #neurons in #brain #microscopy images
#Napari plugin, hugging face, and “also, of course“, #PyTorch

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

I have this silly question about #imagesegmentation. So is there any advantage to using different software for image segmentation? I see #ImageJ, #CellProfiler, #Napari and #Python all can do this, but if the underlying algorithm is the same, then why not just stick with ImageJ?

#napari is a kmage viewer for python, basically an alternative for #imagej. It’s much easier to integrate and extend with plugins (like https://github.com/haesleinhuepf/devbio-napari)

Hello everybody here's my #introduction

I'm a master's student at the University of Constance. I'm currently investigating the spatial localization and the neural basis of multi-stimulus integration in larval Zebrafish using two-photon imaging. For this, I'm wrangling with big amounts of data and performing clustering on time-series of neural responses of single cells. Furthermore, I always try to find new metrics to differentiate neuron populations based on their stimulus reaction to finding the spatial representation of network integration. I am an avid fan of Python and its visualization abilities, which I combine with #napari to show the spatial arrangement of my functional cell clusters.

I'm a big #teamfish member and I love all the weird fish species from all over the world (big #EelOrNoEel fan). My previous work brought me closer to the fascinating genus Neolamprologus and Lake Tanganyika, where I did two months of diving fieldwork.

Outside of science, I'm a big fan of auteur cinema and the Cincinnati Bengals.

Looking forward to building an inclusive community for a scientific discussion about the brain, fish, and everything else with you people here on Mastodon and .

Hello everybody here's my #introduction
I'm a master's student at the University of Constance. I'm currently investigating the spatial localization and the neural basis of multi-stimulus integration in larval Zebrafish using two-photon imaging. For this, I'm wrangling with big amounts of data and performing clustering on time-series of neural responses of single cells. Furthermore, I always try to find new metrics to differentiate neuron populations based on their stimulus reaction to finding the spatial representation of network integration. I am an avid fan of Python and its visualization abilities, which I combine with #napari to show the spatial arrangement of my functional cell clusters.
I'm a big #teamfish member and I love all the weird fish species from all over the world (big #EelOrNoEel fan). My previous work brought me closer to the fascinating genus Neolamprologus and Lake Tanganyika, where I did two months of diving fieldwork.
Outside of science, I'm a big fan of auteur cinema and the Cincinnati Bengals.
Looking forward to building an inclusive community for a scientific discussion about the brain, fish, and everything else with you people here on Mastodon.

RT @kandarpksk@twitter.com

Take part in our 3rd annual @napari_imaging@twitter.com user survey!🚀
This feedback is critical to ensure #napari adjusts strategy according to the needs of the community. You can take the 8 min survey here: http://bit.ly/napari-survey-t. Please share with all napari friends!
#BioImageAnalysis

🐦🔗: https://twitter.com/kandarpksk/status/1600926347756331008

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

Thanks to CZI funding, we will soon have a Research Software Engineer (#RSE) position at the UCL Sainsbury Wellcome Centre to work on #BrainGlobe (https://github.com/brainglobe) and develop #napari plugins.

The post will be based in my RSE team and collaborate with the UCL Centre for Advanced Research Computing.

Happy to chat informally to anyone interested.

Official advert will follow soon. The salary will be UCL Grade 8 (£47k+) for a fixed term of two years in the first instance.

Those interested in scientific visualization (#scivis, #sciviz, #datavis, #dataviz) may enjoy the videos in the #HHMIJanelia Scientific Visualization Interest Group playlist:

https://www.youtube.com/playlist?list=PLfBkfxqisR_dU9RyIeX0I1WbQee86ZTss

These videos include talks from the creators of systems like Agave, ANARI, Datoviz, #napari, Neuroglancer, PyGfx, VizPy, and VMD. Thanks to @billkatz for organizing the series.

Introduction time! ☺️
My name is Florian and I’m a computer scientist and a fully fledged nerd. 🤓

Life pushed me towards the life sciences and now I ❤️ to help others to better analyze their data. 🔬

All we do is #opensource. #CARE #Noise2Void #cryoCARE #FijiSc #napari #AI4Life bioimage.io et al.

I’m so proud of my amazing and amazingly colorful team of #RSEs, and #BioimageAnalysts.

Guess I should also mention: I love #running 🏃‍♂️ and pottery 🥣.

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