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 @ilan-theodoro.bsky.social from my team!
#napari #bioimageanalysis #MCP @biohub
It was meant tongue in cheek, btw. I guess this is @haesleinhuepf.bsky.social dataset, but I am glad to leave my indirect footprint on #napari in this way.
#Napari does a good job promoting the #Tribolium model. 🤔
Fishfeats is a #napari plugin to streamline 3D smFish/RNA quantification with cell/nuclei segmentation, classification etc (running epyseg, cellpose, startdist, and many tools/options/shortcuts for manual corrections)
Everything you need to know: gletort.github.io/FishFeats/
🔬 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 […]
🔬 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.
#napari #Python #ImageAnalysis #DataScience #OpenSource
In our recent blog post, Cornelia Wetzker shares, how she led a project to make bioimage data from fluorescence lifetime imaging microscopy more #fair. She created a plugin for the open-source 3D viewer #Napari that enables the import and analysis of FLIM data.
👉 nfdi4bioimage.de/en/news/meet...
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
Inspired by the ESA's Gaia Milky Way map 🌌!
At SciPy 2023, we showcased visualizing a massive 7.3 TB Gaia dataset on a standard laptop by compressing it to 1.8 GB using #Blosc2. Big data analysis for everyone! 🚀
Dataset: digistorage.es/links/652403...
Paper: www.blosc.org/docs/Explori...
#napari
We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
The materials from the “Reproducible Bio-Image Analysis using #Python, #Napari, #Jupyter, and #AI” workshop, run by @haesleinhuepf.bsky.social as part of the @embo.org Course on #LightSheetMicroscopy, are now available #OpenAccess!
📗 scads.github.io/embo-lsm-bia...
📕 zenodo.org/records/1681...
If you want to try it out, the plugin can be installed from pip:
pip install napari[all] napari-pyflowreg
and allows motion correction as well as basic motion analysis and visualization functionality.
#napari #2P #microscopy #neuroimaging #motioncorrection
I just discovered the “variable graphics memory” option from AMD and Intel and I’m super curious has anyone here tried using it to use your PC’s RAM as GPU memory for AI models?
#GloBIAS #Bioimage #Bioimage_analysis #napari #Microscopy #BioimageAnalysis
Diagnosis of the beep at #LISH25: it wasn't the #HIVEs as such (still room for more users & data!) but the heavy work for the GPU in a warm room: #napari #imaris #CARE #ZEN #slidebook and #MACSiQ software (20 users) on a single GPU making this GPU sweat 😅 💪 We'll now share the load with more GPUs
@scadsai.bsky.social at #LISH25 🔬
On the second day of the @embo.org Practical Course on #LightSheetMicroscopy, @maweigert.bsky.social held a workshop on #MachineLearning for microscopy image analysis. This was followed by a workshop on 3D processing with #Napari from @haesleinhuepf.bsky.social.
We teach also #Napari at #LISH25. By @haesleinhuepf.bsky.social highlighting the awesome power of #Jupyter_notebooks for #reproducibility
Btw, and in the spirit of #OpenScience, all my #Napari #bioimage analysis #tutorials are freely available — from basics to #segmentation, #tracking, and #clustering. Feel free to explore and share ✌️
🌍 www.fabriziomusacchio.com/teaching/tea...
What I really like about @napari.org is how well it integrates modern #Python tools. Great to have such a flexible, evolving #opensource platform for #bioimage analysis! 👌
#Napari #imageanalysis #neuroscience
To wrap this up: Both tools are easy to test. I 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. Curious what impressions and feedback the students will share. 🧪🔍
✍️ 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.
@napari.org
A professional anniversary graphic with a purple background featuring Gonzalo Peña-Castellanos, a smiling man with glasses wearing a plaid shirt. His photo is framed in a circular border with purple and green segments matching the Quansight logo colors. The Quansight logo appears at the top left. Text below the image reads 'Gonzalo Peña-Castellanos, Senior Software Engineer' followed by 'Happy Anniversary! 6 Years at Quansight Labs.
Congratulations to Gonzalo Peña-Castellanos on 6 incredible years at #QuansightLabs! As a Senior Software Engineer and tireless open source contributor, Gonzalo has been instrumental in advancing #JupyterLab, #napari, and numerous Python ecosystem projects. Here's to many more years of innovation!
Two presenters explaining the project of building a common view configuration for enabling the same visualization across spatialdata-plot, napari and Vitessce.
example plot overlaying one image, some annotated points and some annotated geometries, and the exported set of parameters describing how to reproduce the plot.
@mkeller7.bsky.social Sonja Stockhaus @wvierdag.bsky.social @lucamarconato.bsky.social
We started working on developing common view-configurations based on Vega, to improve reproducibility of plots and allow for displaying the same visualization in spatialdata-plot, #napari and #vitessce.
Shoutout to #napari and #kdenlive for making video creation and editing with ~200Gb light-sheet images super easy
Sunny San Diego view
Happy to be in sunny☀️San Diego for ASCB Cell Bio! Tomorrow I will present #Ultrack and #inTRACKtive (poster B513) at 11:15 am. Swing by the CZI+@czbiohub.bsky.social
booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬
#CellBio2024 #ASCB24 #celltracking
🚨 @globias.bsky.social is launching Call4Help: personalized guidance for image analysis challenges! 🌟
📅 1st session: 20–24 Jan 2025
💡 Tools: #Napari, #Ilastik, #CellProfiler
🌍 Expert-led, global time zones
🔗 Apps open 6 Jan. Share your insights:
forms.gle/SSgMXxrto2wV...
#ImageAnalysis
#spatial_transcriptomics #napari #spatialdata
A napari-spatialdata is a bit clunkier than I'd like, but I am slowly getting the hang of it.
#30DayMapChallenge, Day 27: Micromapping
Coyote skull study: used Polycam to create 3D model. Exported point cloud (.laz). Loaded into Napari (video) and Potree (linked).
Model: poly.cam/capture/4FD8...
Potree Viewer: coyote-skull-viewer.netlify.app
#3d #napari #potree #geography
Intro slide for CBIAS 2024 at the Crick. David Barry is standing in front of the audience and talking about a slide with a QR for the programme.
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
6/ 🏆 Within the Virtual Embryo Zoo, users can visualize the tracked datasets with #inTRACKtive, download the complete tracking data (ready to visualize in #napari) and see details of the datasets.
