Peter Sobolewski

Charlie Manuel

HITTIN’ SEASON

Back with the totals and a recap…

Associate Editor or Senior Editor, Nature Methods Title: Associate or Senior Editor, Nature Methods Organization: Nature Portfolio Locations: New York, Jersey City, Shanghai or Beijing Closing Date: August 3, 2025    About Springer Nature Springer Na...

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.

Tensorstore can read/write zarr. It’s been faster than zarr-python, does some different things like commits.

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

a black and white cartoon of spongebob squarepants sitting at a table with a cup of coffee . ALT: a black and white cartoon of spongebob squarepants sitting at a table with a cup of coffee .

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.

GitHub - AlexHego/DL-pixel-classification Contribute to AlexHego/DL-pixel-classification development by creating an account on GitHub.

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/

It really was just a coincidence as far as I know!! 🤯

Davin Potts to the right of a poster titled "Zarr + DragonHPC can acelerate reads from large OME-Zarr microscopy datasets by 3X-300X" At the top is a screeenshot of napari. Below is a diagram of networked data access by Dragon DDict.

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?

Gah! So upset I’m going to miss this because my flight was cancelled today. 😡

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!

YouTube video by LIBRE hub Open Hardware Microfluidics

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...

YouTube video by Euro-BioImaging Communication Image Analysis on high-performance computing | HPC session

🖥 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

OME logo in Red Green and Blue, followed by At sign and letters MBL

#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