sirhc · @sirhc
98 followers · 188 posts · Server fosstodon.org

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: youtu.be/UgNaqbtNJh0

@napari

#napari #yt #yt_astro #astrophysics #data_viz

Last updated 1 year ago

Fabrizio Musacchio · @pixeltracker
314 followers · 205 posts · Server sigmoid.social

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

🌍 fabriziomusacchio.com/teaching

#imageregistration #napari

Last updated 1 year ago

sirhc · @sirhc
94 followers · 183 posts · Server fosstodon.org

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

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.

#yt #datavisualization #napari #opensource #3d #astrophysics

Last updated 1 year ago

sirhc · @sirhc
94 followers · 183 posts · Server fosstodon.org

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

fork ya?

?

#SciPy2023 #napari #icanhazgenerativeytplot

Last updated 1 year ago

Fabrizio Musacchio · @pixeltracker
251 followers · 114 posts · Server sigmoid.social

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

🌎 fabriziomusacchio.com/teaching

#BioImage #napari #OpenScience #ImageAnalysis

Last updated 1 year ago

sirhc · @sirhc
80 followers · 176 posts · Server fosstodon.org

As someone who doesn't do much frontend development, i'm pretty excited that i was able to refactor the 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.

#yt_napari #napari #yt #qt #pyqt #icanhazfullstack

Last updated 1 year ago

sirhc · @sirhc
77 followers · 171 posts · Server fosstodon.org

New video tutorials for the - plugin!

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

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

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

#yt #napari

Last updated 1 year ago

Markus Osterhoff · @mosterh1
73 followers · 454 posts · Server academiccloud.social

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

UA-CPN to segment (natural 😜) in images
plugin, hugging face, and “also, of course“,

#pytorch #napari #microscopy #brain #neurons

Last updated 1 year ago

Matt McCormick · @thewtex
14 followers · 19 posts · Server fosstodon.org

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

forum.image.sc/t/itkelastix-0-

#itk #elastix #MONAI #napari #registration #python

Last updated 2 years ago

Hoang Anh Le (aka Anh), PhD · @AnhHLe2702
219 followers · 193 posts · Server mstdn.science

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

#imagesegmentation #imagej #CellProfiler #napari #python

Last updated 2 years ago

magro · @magro
3 followers · 24 posts · Server muenchen.social

is a kmage viewer for python, basically an alternative for . It’s much easier to integrate and extend with plugins (like github.com/haesleinhuepf/devbi)

#ImageJ #napari

Last updated 2 years ago

Florian Kämpf · @flofightscience
43 followers · 1 posts · Server neuromatch.social

Hello everybody here's my

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 to show the spatial arrangement of my functional cell clusters.

I'm a big member and I love all the weird fish species from all over the world (big 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 .

#introduction #napari #teamfish #eelornoeel

Last updated 2 years ago

Florian Kämpf · @flofightscience
43 followers · 1 posts · Server neuromatch.social

Hello everybody here's my
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 to show the spatial arrangement of my functional cell clusters.
I'm a big member and I love all the weird fish species from all over the world (big 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.

#introduction #napari #teamfish #eelornoeel

Last updated 2 years ago

Francesco Pasqualini · @fspasqualini
123 followers · 154 posts · Server fediscience.org

RT @kandarpksk@twitter.com

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

🐦🔗: twitter.com/kandarpksk/status/

#BioImageAnalysis #napari

Last updated 2 years ago

Albert Cardona · @albertcardona
946 followers · 4 posts · Server mathstodon.xyz

Have you discovered the image processing forum yet? forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software and many more.

#groovy #kotlin #python #java #StarDist #scikitimage #QuPath #napari #ilastik #icy #DeepLabCut #CellProfiler #imagej #FijiSc

Last updated 2 years ago

Adam Tyson · @adamltyson
93 followers · 10 posts · Server mastodon.online

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

#napari #brainglobe #rse

Last updated 2 years ago

Philip Hubbard · @philiphubbard
89 followers · 36 posts · Server qoto.org

Those interested in scientific visualization (, , , ) may enjoy the videos in the Scientific Visualization Interest Group playlist:

youtube.com/playlist?list=PLfB

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

#scivis #sciviz #datavis #dataviz #HHMIJanelia #napari

Last updated 2 years ago

Florian Jug · @florianjug
585 followers · 186 posts · Server mastodon.online

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 . bioimage.io et al.

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

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

#running #bioimageanalysts #rses #ai4life #napari #fijisc #cryocare #noise2void #care #opensource

Last updated 2 years ago

Albert Cardona · @albertcardona
697 followers · 557 posts · Server qoto.org

Have you discovered the image processing forum yet? forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software and many more.

#ilastik #StarDist #FijiSc #imagej #napari #QuPath #scikitimage #java #python #kotlin #groovy #CellProfiler #DeepLabCut #icy

Last updated 2 years ago