@jni@fosstodon.org
@jni@fosstodon.org avatar

jni

@jni@fosstodon.org

Core dev and co-founder napari.org
Core dev scikit-image.org
Co-author elegant-scipy.org
Research Fellow https://www.monash.edu/discovery-institute

Blog https://ilovesymposia.com

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hynek, to random
@hynek@mastodon.social avatar

WAHHHHHHH

jni,
@jni@fosstodon.org avatar

@hynek did you post this as a warning so others on that flight can make alternate arrangements? 😂

vicgrinberg, to Astro
@vicgrinberg@mastodon.social avatar

I just love this image - it highlights why we need all the different telescopes: each of them looks at the same object in different ways. And only when working together a complete image emerges.

Here, 's wide field is combined with 's zoom-in and sharpest IR image we ever obtained, allowing us to study how radiation interacts with interstellar matter.

More here and in the linked articles: ▶️ https://www.esa.int/ESA_Multimedia/Images/2024/04/Webb_captures_iconic_Horsehead_Nebula_in_unprecedented_detail

jni,
@jni@fosstodon.org avatar

@vicgrinberg Absolutely gorgeous.

Do you know how one can get their hands on the raw, full-res images? I'd love to overlay them all in @napari as a demo... 🙏

jni,
@jni@fosstodon.org avatar

@vicgrinberg @napari thanks! yeah re:raw data I presume there are Python libraries to get NumPy arrays from the raw files, and hopefully not too hard to use as a domain novice! 😅😬😬😂

jni, to random
@jni@fosstodon.org avatar

Is there a comprehensive archive, with references, of Elsevier's many sins against scientific progress? @albertcardona @brembs The lead authors of a paper I played a small role in want to submit to Cell 🤢 and I would like to dissuade them.

Follow-up Q: I have a vague vibe that, although the entire traditional publishing system needs to die in a fire, NPG are not quite as scummy as Elsie. Is that vibe justified or not really?

jni,
@jni@fosstodon.org avatar

@jonny @albertcardona @brembs Indeed the basic “all ‘legacy’ journals must die” premise is assumed correct in the question and includes NPG, but I am trying to be realistic about how much I can get in this battle — the authors list is overwhelmingly traditionalist and wary even of preprints. 😞 I'll push for eLife but even that is a stretch. Is it worth steering from Cell to Nature & co? I think so, but I'm worried it's just exposure bias. Profit margins at least seem lower at NPG. (26 vs 38%)

neuralreckoning, to random
@neuralreckoning@neuromatch.social avatar

Early prototype of Mastodon thread viewer:

https://thesamovar.github.io/masto-thread-view/test.html

Just paste the URL of the thread into the box at the top and hit the "linear thread view" button below and it will give you a view of the thread with hierarchical replies sorted by how many engagements they got (reposts + favourites + replies).

It's very early days so it doesn't yet show any images, the design is not ideal, not optimised for mobile, etc. But I already find this useful for getting a feel of big threads.

My aim here is to give people a better way to navigate overwhelmingly large threads and to allow for a sort of archive of interesting threads. If we want to make Mastodon into a viable option for having scientific debates (e.g. alternative to peer review), we need some way to make them more accessible to outsiders and to surface the most interesting and relevant content.

So I'm particularly interested in hearing suggestions for features or other ideas on how to display threads in the context of long lasting discussions with some permanence to them.

At the moment it's just a very simple idea, but I have other ideas for how to display threads that are a bit wackier and I'll add these as extra buttons as and when I work on this. I'm also going to see how feasible it is to make this into a bookmarklet so you can just hit the 'render thread' bookmark in your browser and open a tab with this. Should be straightforward.

If you're interested, please feel free to post suggestions and issues either here or on github: https://github.com/thesamovar/masto-thread-view

May be of interest to @NicoleCRust @jonny

jni,
@jni@fosstodon.org avatar

@jonny @neuralreckoning I’d prefer if most work was client-side or upstream. Per-instance features are kind of annoying, eg coming across mathstodon posts where LaTeX won’t render unless I view them on mathstodon directly. The more the instances diverge, the harder it is for new folks to decide what to join.

Obviously, instances are a great place to experiment. But I just don’t want it to be the endgame…

jni, to random
@jni@fosstodon.org avatar

I love the “reveal” at 2:25. 😍
https://fosstodon.org/@napari/112256746427753857

RL_Dane, to KDE
@RL_Dane@fosstodon.org avatar

My music stopped playing, the phone rang, I answered it.
After speaking for a few minutes, I hung up and the music started up again.

It took me a second to realize that the music wasn't coming from my phone, it was coming from my computer.

is groovy, y'all. It pauses your music when a phone call comes in. (MPRIS-compatible player required, of course, but even mpv on the command line can do that)

jni,
@jni@fosstodon.org avatar

@RL_Dane @a this works really well with a New Zealand accent. 😃

vicgrinberg, to random
@vicgrinberg@mastodon.social avatar

What's your favorite reviews of "Three body problem"? Especially ones that focus on discussing the physics - both in terms of depiction of physics and physicists and in terms of how correct the books are?

Preferably of the Netflix series, but I'll also accept those for the books if especially good on discussing the physics.

Please link to them! Boosts welcome :)

jni,
@jni@fosstodon.org avatar

@vicgrinberg @muellerwhh did you read the later books? I found each a slog (and the sexism in book 2 in particular is 🤢), but the core idea of book 2 is (I think) genius and original, and book 3 is just chock full of outstanding ideas that changed the way I look at the sky. My physics is only from popular physics books but I think I have the basics. (I also 🙄 at the quantum entanglement comms.)

jni, to random
@jni@fosstodon.org avatar

“I haven’t been bitten by Google killing an app or service since Google Reader, because I never again trusted them.”

👆 this.

(Also note: I am aware of Gruber’s terrible takes on the EU, and Threads, and a bunch of other stuff. But on this he is spot on. The Google Graveyard is so damaging to Google’s brand, it’s astonishing to me that (a) anyone still uses Google products, and (b) the execs still kill stuff rather than keeping it on life support just for reputation.)
https://mastodon.social/@daringfireball/112204358739653554

jni, to random
@jni@fosstodon.org avatar

The fun thing is that this Sydney Brenner quote is from 2014, and things have gotten even worse in the past decade. 🙃
https://qoto.org/@enroweb/112150171468524351

simon, to random
@simon@simonwillison.net avatar

I put together some detailed notes showing how I use Claude and ChatGPT as part of my daily workflow - in this case describing how I used them for a 6 minute side quest to create myself a GeoJSON map of the boundary of the Adirondack Park in upstate New York
https://simonwillison.net/2024/Mar/22/claude-and-chatgpt-case-study/

jni,
@jni@fosstodon.org avatar

@simon “I would miss them terribly if they were no longer available to me.” This seems like a good reason to focus on open source, local models, despite their limitations.

(But, as a side note, congrats on llm — the ergonomics are wonderful.)

albertcardona, to vim
@albertcardona@mathstodon.xyz avatar

It's 2024 and most text editors don't have a column-select mode. How can anyone live without it.

jni,
@jni@fosstodon.org avatar

@albertcardona @jzsimon @weberam2 I love vim, but VSCode and PyCharm both also support column selection so now I’m curious — what crappy editor prompted this micro rant? 😂

jni,
@jni@fosstodon.org avatar

@albertcardona @jzsimon @weberam2 Ah you are talking word processors not text editors. ;)

Interestingly I don’t think I’ve ever felt the urge to do this for prose or tabular forms…

tim, to random
@tim@tds.xyz avatar

i have an opportunity to upgrade from 100 Mb/s home internet to 500 Mb/s for an extra $5/mo or 1 Gb/s for an extra $10/mo. I think 500 Mb is probably worth it but my utility curve is already pretty flat tbh. How much internet can one man possibly consume

jni,
@jni@fosstodon.org avatar

@glyph @tim Can Steam actually saturate your bandwidth like that? I’ve found that many centralised services can’t, especially in Australia. (Kudos to Steam if that’s not the case there though.)

luis_in_brief, to random
@luis_in_brief@social.coop avatar

Some days I wonder if, quietly, CC0 is actually a bigger success story than the other @creativecommons licenses put together. Not to slight the other licenses! But CC0 is increasingly catalytic in the library, museum, and data spaces.

https://www.openculture.com/2024/03/the-getty-makes-nearly-88000-art-images-free-to-use-however-you-like.html

jni,
@jni@fosstodon.org avatar

@luis_in_brief @creativecommons I like Dan Cohen‘s CC0(+BY) essay/not-quite-a-license https://dancohen.org/2013/11/26/cc0-by/ and I wish CC would actually implement such a thing already.

jni, to mastodon
@jni@fosstodon.org avatar

One I think underrated aspect of #mastodon is that links go to where they say they go. Not to t.co/bullshit, not to analytics.twitter.com/ayfkm, not anywhere other than the exact link that was posted. You can right-click -> copy link and get the exact link the author shared. ❤️

jni, to SciPy2024
@jni@fosstodon.org avatar

Ok so @SciPyConf @SciPy2024 call for proposals is open (🥳) at https://cfp.scipy.org/2024/cfp! (See also https://www.scipy2024.scipy.org/#CFP for more info.) This year we have a data viz and image analysis track I'm co-chairing and WE NEED YOU 🫵!

This also means I must finally share the 3D scan of The Claw from last year's @scipy2023 lightning talks! You can download it in DICOM or ome-@zarr format from FigShare at https://dx.doi.org/10.26180/25264588! 😂🦀

image/png

jni,
@jni@fosstodon.org avatar

@SciPyConf @SciPy2024 @scipy2023 @zarr in all its 3D glory:

video/mp4

jni,
@jni@fosstodon.org avatar

@SciPyConf @SciPy2024 @scipy2023 @zarr these are the conference Slack posts that threw down the gauntlet claw mitt…

image/png
image/png

grammargirl, to random
@grammargirl@zirk.us avatar

Timeline of a project:

  1. Yes, I can absolutely do that 5 months from now.
  2. I should get started soon.
  3. I should really get started soon.
  4. OMG! OK. Getting started.
  5. I will never make this deadline.
  6. I must change my name and start a new life in Genovia.
  7. Work, work, work, work, work
  8. I might actually make it.
  9. That was easy!

Repeat.

(I am currently at Stage 8.)

jni,
@jni@fosstodon.org avatar

@grammargirl What? I was nodding and laughing all the way to 9, to which I cannot relate. 9 is "never again.", then 10. is "Ooh, this project is for 5 months for now. Perfect duration to start on my new resolution of never leaving things to the last minute ever again. (Goto 1.)"

jni, to random
@jni@fosstodon.org avatar

@simon ok I'm finally trying out your llm library and it's neat. I am intentionally limiting myself to open source and local models. Could you write a post about these? Specifically:

  • strengths/weaknesses of each model?
  • strategies for getting around context length limits? I'm currently interested in text summarisation and immediately hit this with mistral-7b-instruct-v0*
  • yes I did ask mistral itself to suggest strategies but they were distressingly manual and brittle/non-generalisable. 😂
jni, to random
@jni@fosstodon.org avatar

vvCool: new and improved NGFF @zarr support in Fiji, courtesy of @herrsaalfeld and @BogovicJohn:

https://forum.image.sc/t/updated-ngff-support-in-fiji-hdf5-n5-zarr-ome-ngff/91705

Wanna try it out? We just published a small* 3D/3D+t/3D+c+t sample dataset in ome-@zarr** format on FigShare at https://figshare.com/articles/dataset/Data_for_McGovern_et_al_2024_Finding_and_Following_A_deep_learning-based_pipeline_for_tracking_platelets_during_thrombus_formation_in_vivo_and_ex_vivo/25137497 (Jesus sorry for the massive stub didn't know FigShare would use the whole title for the stub 😂)

Want to segment and track it? Check out my 1st PhD student's 1st paper! 👩‍💻🥳 https://www.biorxiv.org/content/10.1101/2023.10.02.560609v2.

*32+GB 😅
**well, we tried, test it out 😅

jni, to random
@jni@fosstodon.org avatar

Nice bioimage analysis job opportunity at Institut Pasteur in Paris:

https://forum.image.sc/t/engineer-in-image-analysis-permanent-posititon-in-institut-pasteur-cdeh-group/91974

#getfedihired

jni, to random
@jni@fosstodon.org avatar

As we are gearing up for the @napari 0.4.19 release (it's coming!!!), @melissawm has pointed me to Astropy’s “Feature freeze frenzy" playlist to play when preparing a release. Pure gold. 😂

https://open.spotify.com/playlist/21VeY0TTrBIvfGNrRoM1YM?si=4fgJf2fISY6kbt8pTRAXig&pi=u-X1RhjFkERnqA

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