Profile avatar
phaips.vd.st
Rubisco phase separation + Cryo-ET PhD @ Engel & Hondele Lab Biozentrum Basel 𝗖𝗛 #TeamTomo
12 posts 216 followers 311 following
Regular Contributor
Conversation Starter
Posts 21 Comments 10

You want to start tomography? Solve structures inside cells? Reach Nyquist 😳 ? @phaips.vd.st and I have a website for you! tomoguide.github.io You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software! Hope it will be useful !

submitted 22 days ago • 3 comments

Hey #TeamTomo, Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging? That's why @florentwaltz.bsky.social and I made this website! tomoguide.github.io Follow the thread 1 /🧵 #CryoET #CryoEM 🔬🧪

submitted 22 days ago • 5 comments

To all #ChlamyDataset enthusiasts, here is a script that lets you directly import the pre-processed results from EMPIAR-11830 into #RELION v5 for subtomogram averaging: github.com/Chromatin-St... #Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience

submitted 30 days ago • 1 comment

🦠🧠 MemBrain update! 🧠🦠 We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics. 🔗 Preprint: doi.org/10.1101/2024... 🔗 Code: github.com/CellArchLab/... 🧵(1/6) #TeamTomo

submitted 34 days ago • 1 comment

Apply now for our international Master of Science in Physics of Life @biozentrum.unibas.ch @unibasel.ch! Scholarships available. More information: www.biozentrum.unibas.ch/education/de... #Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland

submitted 70 days ago • 0 comments

I'm super happy that our story is now published! 📖 www.science.org/doi/10.1126/... But what changed compared to the original preprint? Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.

submitted 68 days ago • 7 comments

In 2004, it took the world a year to add one gigawatt of solar power — now it takes a day.

submitted 72 days ago • 5 comments

einstein sent this to curie in 1911 when she was being harassed by tabloids. it contains everything you’d want in such a letter: (1) your haters are trash (2) you’re a baller, a true queen (3) i have determined the statistical law of motion of the diatomic molecule in planck’s radiation field 🧪⚛️

submitted 335 days ago • 68 comments

To all #TeamTomo #CryoET and #Chlamydomonas aficionados: we have updated EMPIAR-11830 with a bug fix concerning some cryo-CARE denoised tomos as well as additional files and metadata! 🎉👩🏽‍💻 www.ebi.ac.uk/empiar/EMPIA... A little thread about what's new... 🧵 1/n

submitted 89 days ago • 2 comments

💡 At a joint press conference, the #SNSF and its ERI partners called on the Federal Council to abandon the planned cuts to #education, #research and #innovation in the "relief package 27", as they would have far-reaching consequences for the #economy and society. ➡️ https://buff.ly/3CTR2AM

submitted 106 days ago • 0 comments

We (@cellarchlab.com peeps, @manondemulder.bsky.social @phaips.vd.st @fannyleblanc.bsky.social @computingcaitie.bsky.social and Ricardo) had a blast at the EMBO in situ meeting in Heidelberg! Meeting old friends and making new ones! Lots of cool science and new ideas to try 👨🏻‍🔬🔬

submitted 111 days ago • 0 comments

It's a good week for rubisco enthusiasts - very cool preprint from Ron Milo lab www.biorxiv.org/content/10.1... impressive screening of +250 genes spanning available diversity of rubisco, this then used to predict activities of 68,000 known sequences revealing role of phylogeny and habitat

submitted 124 days ago • 4 comments

Exciting update on the CryoET Data Portal! A new annotation set from Mart Last & team is now live. They’ve doubled available annotations with >1,800 tomograms of Chlamydomonas reinhardtii which now have almost fully dense labels, and all can be visualized in the browser using Neuroglancer.

submitted 125 days ago • 1 comment

In case you missed our first webinar of 2025, it is now available. Lorenz Lamm from MUDS - Munich School for Data Science presented MemBrainv2- an end-to-end tool for the analysis of membranes in cryo-electron tomography. https://buff.ly/4hutFwf #SBGridwebinars #ScienceMatters

submitted 125 days ago • 0 comments

Announcing the new bioRxiv dashboard widget - it's now easier to when articles have comments, peer reviews, community discussion, media coverage, videos, and automated analyses 1/2 connect.biorxiv.org/news/2025/01...

submitted 130 days ago • 6 comments

WOW!😍 This is exactly the type of development we hoped the Chlamy dataset would help empower! Lots of organelles and cellular features labeled automatically, context-aware particle picking, & area-selective template matching #TeamTomo 🔬 Big props to @mgflast.bsky.social @thomsharp.bsky.social 🧪🧶🧬

submitted 129 days ago • 1 comment

Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍 Preprint📜: www.biorxiv.org/content/10.1... A short thread🧵👇

submitted 142 days ago • 7 comments

News flash nerds: hornworts are awesome

submitted 145 days ago • 0 comments

More than 1'800 tomograms available for the community. Towards visual proteomics using our favorite organism Chlamy! Check out the preprint: www.biorxiv.org/content/10.1... Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com #TeamTomo

submitted 150 days ago • 3 comments

We are excited to share 71,700 new #Chlamy mutants from the CLiP2 collection pre-publication! Nearly-saturating genome coverage. Please note: new background strain, mating type, and antibiotic resistance. Read: www.biorxiv.org/content/10.1... Search and order: www.chlamylibrary.org

submitted 160 days ago • 1 comment

Entry-level position (80 - 100%) for bioimage analysis specialist at the Imaging Core Facility (IMCF) of the Biozentrum, University of Basel www.biozentrum.unibas.ch/open-positio... @unibas.ch #Biozentrum #Basel #research #science #joboffer #scientific

submitted 167 days ago • 0 comments