Kevin Yamauchi

🔬 studying form and function @ETH_BSSE
🏝️ steering council and core dev @napari_imaging

⛰️⛷🧗

[Lucien Hinderling @lhinderling]

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

[Virginie Uhlmann @VirginieUhlmann]

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):
https://t.co/924OgiNDBn

[Pete Bankhead @petebankhead]

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

[Kevin Yamauchi @ky396]

Nice work, @jobragantini !

[Loïc A. Royer 💻🔬⚗️ @loicaroyer]

📡🧵 Excited to release our preprint: Ultrack: Pushing the Limits of Cell Tracking Across Biological Scales

https://t.co/KN5Hw3BpI0

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.

https://t.co/DvKyowFbbi

#cell_tracking #microscopy #devbio @czbiohub

[Jennifer Waters @JenCWaters]

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 https://t.co/b3Cv9WesTi #microtutor

[Chris Holdgraf @choldgraf]

@PracheeAC @ProjectJupyter @mybinderteam 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.

[Florian Jug @florianjug]

From Images to Knowledge (I2K) is going down @humantechnopole in Milan, Italy, from October 23-25 2024. 🗓️

🚨Abstract and Workshop submission now OPEN 🚨
https://t.co/rdSpJI0YYN

Invited speakers will soon be announced, but most talks will be selected from your🫵 abstracts!!! 📃

[Ben Engel @bengeliscious]

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!🙌

[Romain Guiet @romainGuiet]

It is my great pleasure to officially announce the release of our BIOP-desktop and its documentation 🖥️📖🔬 🎉 more on the forum https://t.co/qztwkA9ruj
#bioimageanalysis #docker #jupyterlab @EPFL_en @epflSV @LeBIOP

[Lucien Hinderling @lhinderling]

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

[Rita Strack @rita_strack]

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.

[napari @napari_imaging]

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: https://t.co/NGssYqdeZc

[Norman Rzepka 🇺🇦 @normanrz]

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.
https://t.co/1FeYKxaAZl
@openmicroscopy @zarr_dev

[Kevin Yamauchi @ky396]

Nice work @Albertdm99, @martweig , and co-authors!

[Martin Weigert (maweigert.bsky.social) @martweig]

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 https://t.co/UKooR3wV0V
https://t.co/n3ZNfNaMvG

[Eric Topol @EricTopol]

"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."
https://t.co/ddafMtac9i @bengeliscious @biozentrum @svenklumpe
@EM_STP

[Giotto @GiottoSpatial]

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. https://t.co/28IbF8eU5L

[Joel Lüthi @joel_luethi]

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: https://t.co/xNOs1sJIbE

[Jordão Bragantini @jobragantini]

Just launched v0.2.0 of our cell tracking tool 🚀 Check out our GitHub repo: https://t.co/6ngaD9j5L9! Seamlessly combines segmentation & tracking via Python API 🐍 Scales effortlessly to handle massive datasets, like the #zebrahub paper. #CellTracking #Bioinformatics

[Nils Eling @NilsEling]

Very excited that our "End-to-end workflow for multiplexed image processing and analysis" has now been published in @NatureProtocols https://t.co/gdNYgIOA5U @JonasWindhager @BodenmillerLab