For last 10 years - we have worked with thousands of organizations around the world helping support them in integrating foldscope programs. To bring in a new cohort of organizations - we are re-launching “fast and curious” 2025 edition - apply and get a Foldscope trainer and Foldscopes for free!

Fly Jordan Fly!! #GoBirds

The myth of the lone genius in science actively undermines the conditions that foster real progress - these people exist but they have limits and true innovation requires scaling beyond the individual

#HappyFluorescenceFriday! #microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications! Learn more & sign up: buff.ly/esGIotD

And here we are, the first book live on Amazon. A "Nobel in Chemistry coloring book" :D All 116 Nobels (3 books) have been hand-drawn and are ready to be colored. Part 2 is on its way, and Part 3 will be released after this year's Nobel Prize. www.amazon.com/dp/B0FRF39YS4 #chemsky #nobel

Flying out of San Jose buzzing after @chanzuckerberg.bsky.social #ImagingTheFuture. Amazing to shake the hands of long time insprations: @andrewgyork.bsky.social @makertobey.bsky.social @manorlaboratory.bsky.social & new ones like Gustavo Menezes—plus catching up with friends & collaborators!

From #ome-ngff-validator you can open open #OME-Zarr images in a bunch of viewers, and neuroglancer's rendering of multi-channel images just got a lot nicer: ome.github.io/ome-ngff-val... - See github.com/google/neuro...

new blog post: in which I talk (briefly) about getting a new job and moving back to Europe, getting a VPS, and self-hosting my code and my personal website. pages.erickratamero.com/personal-web...

KYLE SCHWARBER

Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects! My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally. Check out my portfolio and contact: acorbat.github.io

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)

🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:

Delighted to welcome @tracykteal.bsky.social as the CEO of @openrxiv.bsky.social - Tracy brings a wealth of experience in non-profit leadership and open science to the the team, and we're all so excited to be working with her openrxiv.org/announcing-c...

🚀 napari 0.6.4 is out! Highlights from this bite-sized release: launching scripts from the command line with `napari <path-to-script>` and making the console auto-focus when opened. We’ll be announcing all future napari releases here, so stay tuned! 🔗 Release notes: napari.org/stable/relea...

Excited to share our new @pubs.acs.org paper! We engineered cells with ~10% photolipids in the ER membrane. This enabled optical control of membrane viscosity to study its impact on ER→Golgi protein transport. @dirktrauner.bsky.social @noemijimenezrojo.bsky.social pubs.acs.org/doi/10.1021/...

Abstract submission #CBIAS2025 is closing on August 31st - we invite submissions on all topics related to #bioimageanalysis: new tools, biological discoveries using existing methods, and anything in between. Early-career researchers especially encouraged to submit! www.crick.ac.uk/whats-on/cri...

A really nice interview with Juan. Important messages: - "I think that universities are missing a trick in not investing more in this type of work [open source software development]" - "Never code alone."

HITTIN’ SEASON

Back with the totals and a recap…

Nature Methods is also hiring to replace me (applications close August 4th!!!) and I will do everything I can to support their next bioimaging editor (ask me anything!). springernature.wd3.myworkdayjobs.com/SpringerNatu...

Teach your #microscope how to print: Low-cost rapid-iteration #OpenSource #microfabrication for #biology: -no cleanroom -replace SU-8 #photoresist & silicon wafers by #3Dprinting #resin & microscope slides - #fluorescence microscope-based maskless #photolithography doi.org/10.1039/D5LC... #DIYbio

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇

@napari.org @jni.codes is a finalist in the @ardc.edu.au Eureka Prize for Excellence in Research Software. Learn more: youtu.be/0g_MkTa_NwQ #EurekaPrizes

Cell tracking is never perfect, and it's important to understand the types of errors your solution contains. Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d... You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.

first data from the new LLSM in PertzLab @olivierpertz.bsky.social! i always thought nuclei were spherical but they are pancakes???? so much more to see in 3d, but data volume produced is insane, we will have to rethink our analysis pipelines. tips welcome! here shown in @napari.org

The emptiness of wanting a final sip of coffee and picking up the mug and realizing you already drank it all

Thank you @prefix.dev and Astral (tagging @crmarsh.com as the company isn't on Bluesky AFAIK) for bringing these tools to scientists everywhere far faster than I expected! Also thanks to @snarky.ca and everyone else who thought, worked, and pushed hard to get standards and people moving.

Great to see @alexhego.bsky.social share instructions on a DL pixel‑classification problem we worked on at image.sc. If you’re working on a challenging 3D DL semantic‑segmentation problem and need more options than most tools provide, check out this repository. github.com/AlexHego/DL-...

Harper and Schwarber both hot at the same time? Inject this right into my veins! #GoPhils

happy to finally share what we've been cooking 🍳

First day of #bobiac2025. Six days of intensive Python based #BioImageAnalysis. Intro by @fedegasparoli.bsky.social - "This will be a long week, but it will change your life". iac.hms.harvard.edu/bobiac/2025/

Favorite #SciPy2025 moment (so far?): poster by Davin Potts on speeding up HPC file IO for #Zarr files and involving napari and the awesome @jookuma.bsky.social‬ I met Davin's son at SciPy 2024 and demo'd napari and introduced him to Jordao 🤯 Butterfly effect?

Zack. Wheeler. WOW #GoPhils

A modular hand-held #OpenSource #fluorescent #camera unit for #wound #imaging: -custom #3Dprinted housing -based on #RaspberryPi & #ArduCam 21MP -3 independent #LED channels doi.org/10.1038/s420... #DIYbio #lab #instruments #fluorescence #microscope #microscopy #NO #pH #ML #medicine

it was already fun to look around the documentation for cmap (cmap-docs.readthedocs.io) but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂 as a mild deutan myself, I appreciate it! 🙏

I'm really looking forward to getting to teach this tutorial with @ruben-arts.bsky.social and John next week at #SciPy2025! This has been fun to collaborate with them on to create. I hope tutorial participants enjoy it and come away feeling they have a whole new toolkit to empower themselves with!

A few weeks ago, I gave an overview talk on our efforts in making Open Hardware Microfluidics. The talk is now online here: www.youtube.com/watch?v=DP6L... Thanks to @makertobey.bsky.social @ LibreHub for the invitation :)

🧑‍🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab 📜: zenodo.org/records/1575... 👨‍💻: github.com/HenriquesLab...

🖥 How can bioimaging facilities scale analysis & ensure FAIR data provision? At #ImageData Community Days, we explored high-performance computing at @vschpc.bsky.social + KU Leuven’s IT infrastructure for bioimage analysis. @sebastianmunck.bsky.social 🎥 Watch: youtu.be/XWmsOlbSdtQ

This is so cool.

Core facility contributions are essential, and #ImagingScientists deserve to receive #CreditWhereItsDue. That’s why we fully support the #AcknowledgementGuidelines launched by @royalmicrosoc.bsky.social and @globalbioimaging.bsky.social and have proudly displayed them in our digital office.

Amazing lol

The Executable Books team and @curvenote.com are doing some of the most impressive things in the scientific publishing space at the moment. I'm so happy and thankful that Curvenote are once again partnering with @scipyconf.bsky.social to support the #SciPy2025 proceedings! :D

#microscopycommunity- do you use BioFormats, OMERO, OME-TIFF, OME-Zarr or are you interested in open source and microscopy? Then you should check out the recordings from OME2025! buff.ly/fgUxoQf @openmicroscopy.org @gerbi-gmb.de‬. @jacksonlab.bsky.social‬ @mblscience.bsky.social

This is the closest I will probably ever get of the original ‘napari’ 😄 To be exact: 1940.421 km away✈️ @napari.org

Ever wondered how Conda and Pixi "know" to install CUDA packages only on GPU machines? 🤔 Meet virtual packages - a clever solution to inject system compatibility information to the SAT solver to ensure compatibility. prefix.dev/blog/virtua...

FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging Let's have a look 👇🧪💻🔬

I gave in! After students asking for it, I now made a simple figure design checklist. To help all scientists w/o graphic skills create clear, accessible, and truthful charts! -> Out in @nature Cell Biology: rdcu.be/erwl4 #DataVisualization #PhD #SciComm Thx for review @bethcimini.bsky.social + 2

#Microscope Upcycling: Transforming legacy microscopes into #automated #cloud-integrated #imaging systems: - #OpenSource automation: X-Y positioning, focus stacking, img acquisition/storage - cost: US $300 doi.org/10.1016/j.oh... #DIYbio #lab #instruments #microscopy #Raspi #PiCam #Python #OpenCV

As AWS open source just turned our request down, anyone have contacts at Google Cloud or Microsoft Azure who thinks they might be interested in donating cloud credits for an educational tutorial at SciPy 2025?