psobolewskiphd.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Starved of #Phillies highlights? John has you covered! #GoPhils

submitted 3 days ago • 0 comments

If the block on the Federal Register isn’t removed in the next few months, I fear a majority of labs will close within a year. This small procedural wrench has the power to kill US science indefinitely, losing an entire generation of discovery and innovation.

submitted 6 days ago • 25 comments

Our next community meeting is coming up! Join us at 9am CET (Paris/Warsaw/etc) / 1:30pm IST (Delhi) / 7pm AEST (Melbourne). Zoom: numfocus-org.zoom.us/j/8335164262... Agenda: hackmd.io/9vo_DiJpSfuU... What is this meeting for? 🧵👇 (1/4) #Python #SciPy #imaging

submitted 7 days ago • 1 comment

💡 Looking for #FacultyPositions in Europe? The search can be a maze! I shared my personal journey in this @cp-matter.bsky.social article, thanks to an invite from @cranfordmatter.bsky.social. 🔓 Free access here 👉 authors.elsevier.com/c/1kZ4b9Cyxd... #chemsky #AcademicLife #CareersInScience

submitted 7 days ago • 0 comments

‼️🔬 We start!!! 🎉🤖 Super exciting!!! After years of teaching courses for #DeepLearning for Microscopy and Life Science application, we start today our first “advanced course” @embl.org! #EMBLDeepLearning

submitted 8 days ago • 2 comments

The 10th #RSCPoster is going to be here in 2 weeks. We've seen lots of growth and change over the last 10 years and I can't wait to see what's coming next! An incredible event that is not to miss so make sure you sign up now and get involved (on LinkedIn) on the 3 March www.rsc.org/our-events/r...

submitted 8 days ago • 0 comments

🎤 Another speaker joins #TiM2025! We’re thrilled to announce @ritastrack.bsky.social as a new speaker, delivering an exciting talk on Wednesday. Huge thanks to her for joining us! Stay tuned for more updates on our TiM page: bit.ly/3BPN9fB

submitted 12 days ago • 0 comments

🔬 Are you looking to work in an imaging core facility? 🔬 Permanent Staff Scientist position at the UEF Cell and Tissue Imaging Unit at the School of Medicine, Institute of Biomedicine in Kuopio, Finland. uef.varbi.com/en/what:job/...

submitted 12 days ago • 0 comments

After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...

submitted 13 days ago • 12 comments

Hi folks! napari is officially on bsky now! 🥳 Let's hit the ground running with a reminder that all are welcome at our next (Atlantic) community meeting on Feb 12, 8:30am SFO / 11:30am NYC / 5:30pm Paris. Agenda and details here: hackmd.io/BXWDZ3i8Q6OA...

submitted 14 days ago • 1 comment

Amazing new #Python #PEP to improve optional dependencies handling: https://peps.python.org/pep-0771/ The PEP is very thorough and well-written, and it perfectly uses @napari as a motivating example. We were not involved but we fully endorse it! 😃

submitted 16 days ago • 1 comment

Final: Wet Spot 1, Duke 0 Big win for Wet Spot, who gives Duke its first ACC loss. Clutch defense on Cooper Flagg late, forcing the turnover on a potential game-tying shot.

submitted 17 days ago • 2 comments

The OME Community Meeting, which has always be in Europe, will be at MBL this year! It's a unique opportunity for people this side of the pond who are working with open-source microscopy data. Travel grants available for NA-based folks until Feb 12th! www.bioimagingnorthamerica.org/events/ome-2...

submitted 20 days ago • 1 comment

If you use mkdocs for your python docs, and want quick full API autogen (with navigation) try github.com/tlambert03/m... Particularly if you currently use the mkdocs-gen-files/literatenav/custom-script approach

submitted 20 days ago • 0 comments

📢 Submissions are now open for the CellMap Segmentation Challenge. Build the best method for segmenting cellular organelles in vEM using our 289 annotated volumes, 40 organelle classes, and 22 diverse cell and tissue types. 🔗 hhmi.news/410evJQ

submitted 20 days ago • 1 comment

A long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it. www.science.org/content/blog...

submitted 21 days ago • 21 comments

🎙️ Global BioImaging Train-the-Trainer 2025 Course is open for applications 📅 17-21 November 2025 📍 Melbourne, Australia ⚫ Course for imaging core facility professionals to organize and deliver effective training programs ⚫ Travel grants available globalbioimaging.org/internationa...

submitted 22 days ago • 0 comments

Bioimage analysis professionals: join us in-person for a workshop at ISTA in Klosterneuburg, Austria, April 7–8, 2025. A workshop to adapt and expand the current Data Carpentries image processing curriculum. Information & registration: tinyurl.com/3twkax2k

submitted 22 days ago • 1 comment

Probably a good time to remind my American friends that my institute here in Milan is recruiting broadly for everything from the postdoc to group leader level, and we have visa and immigration support 🇪🇺.

submitted 23 days ago • 1 comment

If you're a basketball fan, particularly an #ACC basketball fan, you really gotta read @bgeisinger.bsky.social Tremendous explanations of offensive & defensive actions with graphics & videos. You'll understand more of what is going on on the court, which helps you appreciate good process. #XsAndOs

submitted 24 days ago • 0 comments

🙏 If you have a @github.com repo that has a docs (or other website): PUT A LINK IN THE REPO "ABOUT" SECTION 🙏 Also: 🙏 ENSURE I CAN RETURN TO THE REPO 🙏

submitted 25 days ago • 0 comments

I put together a small guide on how to get started with Fiji. Please distribute to anyone who might benefit form this! zenodo.org/records/1477... #imageanalysis #fiji #imagej #training

submitted 26 days ago • 5 comments

My latest project lets you explore the entire commit history of any GitHub repo ✨ Obviously, D3.js was one of the 1st repos I tested. You can clearly see the 3000+ commits made by its creator @ocks.org! But also @fil.rezo.net & many others. nbremer.github.io/ORCA/commit-...

submitted 28 days ago • 3 comments

🌍Whether you are located in America, Europe, Asia, Africa, or Australia, you are invited to apply for the ASAPbio Fellows Program and drive open science conversations in your community. We offer: ✅Training on preprints ✅Support for delivering a local talk ✅Opportunities to collaborate on projects

submitted 31 days ago • 1 comment

This one is mostly about the title subject (featuring a very interesting compound from academia) but it’s also about attacking the NIH:

submitted 32 days ago • 4 comments

Here’s the radiolarian model after removing the supports #sciart #3dprinting

submitted 32 days ago • 27 comments

Why do so many packages store massive files (models, atlases, etc.) per user? The same 70GB for 10 users = massive waste. We need a cross-platform standard for downloading and system-wide caching of immutable files from URLs. Imagine: immut://zenodo.org/records/12345/stuff.h5. Does this exist?

submitted 36 days ago • 0 comments

Wow! Two epic games today, emotional roller coasters! Super happy with both outcomes! #GoBIlls #FlyEagles

submitted 37 days ago • 0 comments

We developed an interactive tool that can be used in undergraduate inorganic chemistry to predict IR/Raman activity! Very proud of Mary Ayeni and Ignacio Migliaro for their efforts, and thankful for Mohammad Omary for another collaborative success. pubs.acs.org/doi/10.1021/...

submitted 39 days ago • 0 comments

Registration is OPEN for the 2025 QuPath Training Course on Feb 24-25 and an Advanced Users Meeting on Feb 26 at @lji.org . The year, the focus will be on Multiplex Immunofluorescence analysis. Hosted by Zbigniew Mikulski, @iamichaelnelson.bsky.social , and myself.

submitted 43 days ago • 1 comment

I'll never grow old of looking out the window; plane or train.

submitted 44 days ago • 0 comments

Quantitative Imaging From Acquisition to Analysis applications are due Jan 31! 2 weeks of total microscopy & image analysis immersion with me, @talleylambert.bsky.social, @bethcimini.bsky.social, @florianjug.bsky.social & Hunter Elliott! See comments... (1/5) meetings.cshl.edu/courses.aspx...

submitted 47 days ago • 4 comments

I released the LUT finder: A plugin to see all your ImageJ / Fiji LUTs in a table with previews, auto generated descriptions and filtering! You can try it with the KTZ_LUTs update site or from github.com/kwolbachia/L.... I'm looking for your feedbacks! #FluorescenceFriday #MicroscopyMonday

submitted 47 days ago • 2 comments

Looking for a place to start your lab, or a join an existing team as a permanent researcher? My Institute, the INP in Marseille, has multiple open positions: associate professor, lecturer, group leader. Check more here, happy to answer questions by email or DMs! euraxess.ec.europa.eu/jobs/304107

submitted 47 days ago • 2 comments

Join me, @talleylambert.bsky.social, @bethcimini.bsky.social, @florianjug.bsky.social & Hunter Elliott for our two week CSHL course on microscopy & image analysis starting March 24, 2025! Applications are due 1/31/25. meetings.cshl.edu/courses.aspx...

submitted 49 days ago • 1 comment

Reposting my offer for 1-1 mentoring for anyone… email me and we'll find a time! Especially happy to talk with those from diverse backgrounds and non-traditional career trajectories.

submitted 54 days ago • 1 comment

And to start 2025 strong… Our work #NanoPyx is out in Nature Methods 😍❤️ DOI: doi.org/10.1038/s415... #NanoPyx is a Python framework that uses the #LiquidEngine to efficiently accelerate bioimage analysis for any user! (1/n) ⬇️

submitted 54 days ago • 3 comments

Happy New Year! 🎉 If your 2025 resolution is to finally get your lab life together (read: #NewPIs), you’re not alone. A few people have requested I share how we use automation to survive: 1️⃣ Recruitment & Scheduling 👩‍🔬 2️⃣ Finance & Ordering 💸 3️⃣ Alerts & Emergencies 🚨 So here goes!—A 🧵... 1/n...

submitted 55 days ago • 5 comments

We’ve launched our new blog to share insights, tools, and stories from our lab life. Our first post is live: “New Year, New Lab: Automating Your Lab Life with Zapier.” Learn how we use automation to manage the chaos and focus on science. 🥼🤖 Check it out here 👉 chorylab.substack.com

submitted 55 days ago • 2 comments

I made some updates to the tiled rendering branch in @napari. If you have uv installed, then this should open the mouse liver FIB-SEM dataset from OpenOrganelle: uv run https://atrium.kyleharrington.com/visualization/napari-tiled-zarr/0.0.3.py s3 […] [Original post on mastodon.social]

submitted 58 days ago • 0 comments

Currently working on improving the JupyterLab code consoles, to be able to change the position of the prompt cell and not clear code on execute. This would allow for more use cases such as a "Single Cell" usage, while leveraging all the features the console already provides ✨

submitted 60 days ago • 0 comments

Fun game comparing monospaced fonts: https://www.codingfont.com JetBrains and Fira were my top two. HT @gruber.foo

submitted 61 days ago • 0 comments

Coding in Python and looking to perform bulk RNA sequencing analysis? With pytximport recently published in Bioinformatics and version 0.11.0 out today with many improvements, it’s time for my first Bluetorial! A thread 🧵 (1/12)

submitted 88 days ago • 3 comments

🥳Alrighty - end-of-year push to get the final version of #CellSeg3D out! 👩‍💻 pip install napari-cellseg3d==0.2.2 📚 biorxiv.org/content/10.1... We extended benchmarking, new videos, extended text, and a demo on cFOS 👋

submitted 64 days ago • 1 comment

Oof, software releases are always so nerve racking 😅 just updated bento-tools.readthedocs.io to v2.1.4 🥳 We now support 1-to-many spatial indexing for mapping cells to multiple organelles/subcellular domains, enabling the modeling of complex spatial relationships! #spatialbiology 🧪🧬🖥️

submitted 69 days ago • 2 comments

New Year, new job? Delighted to announce two early-career-level (post-BA/BS or MA) positions in my lab, and an open call for computational postdocs at the Broad! First, an image analysis associate - work on high content screens for all kinds of cells and dimensionalities! See more at link (1/4)

submitted 71 days ago • 2 comments

Want to 3D print a pipette holder for Gilson and Eppendorf pipettes? New design by #IanKercher. www.printables.com/model/109822...

submitted 71 days ago • 0 comments