We've spent the last year building something at @humantechnopole.bsky.social that we think is genuinely needed: #AI that works across biological scales and data modalities, not just within them. A thread on what we're doing, why, and who we're looking for. A 🧵... 1/9
Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package:
- fully bootstrapped Java setup (just pip install)
- lazy, repeatably-indexable Array object
- fully spec-compliant OME-Zarr group obj.
- xarray/dask exports
github.com/imaging-form...
v0.0.rc1 on PyPI
One of the funniest conversations I've ever had with Claude...
stick with it through the third image to watch it slowly realize it's broken, try to "play it cool", fail spectacularly, then attempt self-aware commentary and immediately faceplant again.
it's worth it, I promise.
📣 We are accepting applications for the 2026 Boston Bioimage Analysis Course (BoBiAC): bobiac.github.io! Join us this July at Harvard Medical School for a 6-day intensive hands-on course to learn bioimage analysis with Python!
Apply by May 18th! No prior Python experience required!
🧫->🔬->💻->📊
QI Class of 2025! Centroid = @sciencedoodles.bsky.social & @florianjug.bsky.social / first minima = @talley.codes & me.
Applications for 2026 due on Friday!
meetings.cshl.edu/courses.aspx...
🔬 🖥️ Applications are open for the CSHL course Quantitative Imaging: From Acquisition to Analysis (April 6–21, 2026)!
An intensive, hands-on course covering advanced fluorescence microscopy and quantitative image analysis using open-source tools.
🗓️ Apply online by Jan 30, 2026
well, I'm biased... but i think absolutely! 😂
WAY more things in the database (like 1000s more). more FPs, dyes, filters from all providers. (The thermo viewer is primarily their own products). share/restore/download state.
plus, it's open source, non-commercial, and accepts contribs
try it? 👍
Indeed! Was broken. Fixed now
Will have a look!
It’s actually neither, it’s np.zer<TAB>
there quite a bit of `@Todo` in my checks still
Excellent! Thoroughly enjoyed.
(And it was cool to learn where the inspiration for your cmap PRs came from 😄… nice integration!)
Just played a bit with ty docs.astral.sh/ty/
I’m drooling anticipating the day when the last slow pre-commit hook (mypy/pyright) falls and the entire check is blazing fast ⚡️💨
Maybe not just yet… but so soon
ugh. the macos Tahoe border radius is killing me
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! 🙏
Gotcha. That sounds nice!
I’ve definitely been very happy with gh copilot agent as well, particularly with sonnet 4. my comment was as much about the humorous failure modes :)
Wouldn’t that depend as much (if not more) on the underlying model than the agent extension?
i'm generally thrilled with gh copilot agent recently.
There have been multiple very funny cases though where I have asked it to fix a broken test, and the "fix" came in the form of simply deleting the problematic test 😂
"well ... the tests PASS now don't they??"
😂
I think there’s a good degree of personal preference and subjectivity here. I like magenta here as indicating “danger” more than blue. But there would also be nothing wrong with blue, in terms of visibility
please accept this PR
```
:root {
--bgColor-danger-emphasis: magenta !important;
--fgColor-danger-emphasis: magenta !important;
--bgColor-danger: magenta !important;
--fgColor-danger: magenta !important;
}
```
custom github css
for you other colorblind coders out there, tired of missing the red X in your github actions logs
.color-fg-danger, .fgColor-danger {color: magenta !important;}
.octicon-x {color: magenta !important;}
you're welcome
Immunofluorescence image of a mouse brain slice, with nuclei (magenta) and microglia (orange) shown.
Zoomed in Immunofluorescence image from the full mouse brain slice, with nuclei (magenta) and microglia (orange) shown.
Steven has our Snouty-OPM running again after our lab move. He added projection mode, sensorless AO, and a new control GUI based on @talley.codes + crew's pymmcore-plus/pymmcore-gui. Here are some IF-labeled microglia (orange) in the middle of an uncleared 60um mouse brain slice. No deconvolution!
Our openSPIM is officially up and running to image the latest catch of the day! Fueled by pymmcore-plus & pymmcore-gui! 💪⚡🔬 pymmcore-plus.github.io/pymmcore-plus/ github.com/pymmcore-plu...
💻 Announcing the Boston Bioimage Analysis Course — BoBiAC!
Join us this July at Harvard Medical School in Boston for a 6-day deep dive into bioimage analysis with Python, hosted by the IAC and CITE.
Apply by May 16th, 2025!
Ah! Were we lucky enough to entice @pawamoy.bsky.social to Bluesky? :)
