Joined February 2009
- Tweets 195
- Following 144
- Followers 306
- Likes 309
6 Photos and videos
Kevin Yamauchi retweeted
18 Sep 2024
Huge update to Convpaint, and preprint out on bioRxiv!
We develop a pixel classifier similar to Ilastik, but built for napari & with technical improvements. Now even works on animals! 1/10
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Kevin Yamauchi retweeted
17 Sep 2024
Everyday is spline day, and today even more! We are releasing #SplineBox, a Python package for spline fitting 🐍 Fantastic collab with the @EPFL_Imaging Center building on my @emblebi work. Check it out, feedback welcome (love letters or angry e-mails):
splinebox.readthedocs.io
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Kevin Yamauchi retweeted
11 Sep 2024
Let me introduce: InstanSeg 🦠🔬💻👩🔬
This *would* have been a short thread about Thibaut Goldsborough’s PhD work… but he solved too many problems.
Now it's a long thread about 2 preprints, a whole new approach to cell segmentation & #opensource software to make it easy to use
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4 Sep 2024
Nice work, @jobragantini !
3 Sep 2024
📡🧵 Excited to release our preprint: Ultrack: Pushing the Limits of Cell Tracking Across Biological Scales
doi.org/10.1101/2024.09.02.6…
A tour-de-force by @jobragantini, #Ultrack is a versatile, highly accurate, and fast ILP-based cell tracking software for 2D, 3D, and multicolor datasets. It has convenient @napari_imaging and @FijiSc plugin interfaces and built-in HPC cluster support.
github.com/royerlab/ultrack
#cell_tracking #microscopy #devbio @czbiohub
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Kevin Yamauchi retweeted
8 Aug 2024
Introducing Microtutor LIVE! Work through a Microtutor imaging course on your own schedule & meet with instructors virtually for Q&A. 1st course on Fluorescence Microscopy is scheduled for the fall! FREE & open to all! More info & apply at tinyurl.com/microtutorlive20… #microtutor
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Kevin Yamauchi retweeted
25 Apr 2024
And to be clear this isn't just @ProjectJupyter , the whole scientific python ecosystem is in an even more brittle state. There are millions of dollars flowing into research/education efforts that *use* them, but almost nothing flowing to the projects themselves.
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Kevin Yamauchi retweeted
5 Apr 2024
From Images to Knowledge (I2K) is going down @humantechnopole in Milan, Italy, from October 23-25 2024. 🗓️
🚨Abstract and Workshop submission now OPEN 🚨
forms.gle/E2McVjKU1sAsF97Q9
Invited speakers will soon be announced, but most talks will be selected from your🫵 abstracts!!! 📃
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Kevin Yamauchi retweeted
11 Apr 2024
1800 tomos of everyone’s favorite #Planimal🌱 are online to browse in molecular detail. We hope this will be a resource for methods development and new biological discoveries. Shout out to @AbhayKot & team, @MPI_Biochem, and our @biozentrum group (Ricardo🙏). Huge team effort!🙌
The new @EMDB_EMPIAR cryo-electron tomography (cryo-ET) browser allows you to see proteins up close in the cellular environment.
Over 1,800 high-resolution reconstructed tomograms from cryo-plasma-FIB milled Chlamydomonas reinhardtii cells are available.
ebi.ac.uk/about/news/announc…
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Kevin Yamauchi retweeted
9 Apr 2024
It is my great pleasure to officially announce the release of our BIOP-desktop and its documentation 🖥️📖🔬 🎉 more on the forum forum.image.sc/t/biop-deskto…
#bioimageanalysis #docker #jupyterlab @EPFL_en @epflSV @LeBIOP
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Kevin Yamauchi retweeted
22 Mar 2024
Stem cell colonies from @PertzL 🤝 interactive data visualisation in @napari_imaging. Segmentation, tracking, single cell signalling states... So much fun to explore and search for patterns this way
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Kevin Yamauchi retweeted
20 Mar 2024
I have been helping handle spatial omics papers for the past year or so, both experimental and computational, and this was a great one! I think SpatialData will be a one-stop shop for many working in SRT and spatial omics.
20 Mar 2024
Out today from the Stegle, Theis, and Moore labs! SpatialData is a user-friendly computational framework for exploring, analyzing, annotating, aligning and storing spatial omics data that can seamlessly handle large multimodal datasets.
nature.com/articles/s41592-0…
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Kevin Yamauchi retweeted
2 Mar 2024
Curious about contributing to napari? Core developer @WVierdag is leading our all-new napari code cafés! (™️) The first one is this Wednesday at 8pm CET (Paris) time. Improve our screenshots to be pixel perfect, or turn your own idea into reality! Details: forum.image.sc/t/napari-code…
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Kevin Yamauchi retweeted
16 Feb 2024
I posted an RFC for #OMEZarr to adopt Zarr v3. I am currently looking for endorsements. If you want to see OME-Zarr use the new Zarr version and sharding, please let me know and I'll add you to the list of endorsers.
github.com/ome/ngff/pull/227
@openmicroscopy @zarr_dev
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7 Feb 2024
Nice work @Albertdm99, @martweig , and co-authors!
Excited to share Spotiflow, our new spot detection method for image-based spatial transcriptomics that facilitates the analysis of large iST images. Lead by @Albertdm99 jointly w @GioeleLaManno @epflSV @EPFL_Imaging @EPFL_BioE biorxiv.org/content/10.1101/…
github.com/weigertlab/spotif…
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Kevin Yamauchi retweeted
1 Feb 2024
"We are standing on the cusp of a new era of biology, where the integration of multimodal structural datasets with multiscale physics-based simulation will enable the development of visible, virtual cells."
cell.com/cell/fulltext/S0092… @bengeliscious @biozentrum @svenklumpe
@EM_STP
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Kevin Yamauchi retweeted
29 Nov 2023
Dear spatial afficionados, check out our latest contribution to the spatial data analysis landscape. In this work we present Giotto Suite, our completely new ecosystem designed to work with the most exciting and challenging spatial datasets. biorxiv.org/content/10.1101/…
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Kevin Yamauchi retweeted
15 Nov 2023
Last week, we had an amazing #OME_NGFF_hackathon focused on next generation bioimage analysis workflows. We had 45 community members at the hackathon 🎉
Interested to learn what happened there? We made an overview of the hackathon outcomes here: forum.image.sc/t/outcomes-of…
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Kevin Yamauchi retweeted
18 Aug 2023
Just launched v0.2.0 of our cell tracking tool 🚀 Check out our GitHub repo: github.com/royerlab/ultrack! Seamlessly combines segmentation & tracking via Python API 🐍 Scales effortlessly to handle massive datasets, like the #zebrahub paper. #CellTracking #Bioinformatics
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Kevin Yamauchi retweeted
19 Oct 2023
Very excited that our "End-to-end workflow for multiplexed image processing and analysis" has now been published in @NatureProtocols go.nature.com/3s1sdxt @JonasWindhager @BodenmillerLab
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