jni

jni, 2 hours ago to random

Hey #OpenScience advocates! Ever had the feeling that you wanted to download all of your open science / research software #RSE #RSEng thoughts into a collaborator/grad student's brain, but your regular coffee catchups aren't cutting it??? Just point them to this new #SummerSchool from the awesome @madicken!

https://urssi.us/blog/2024/05/20/applications-now-open-for-a-summer-school-in-open-science--research-software-engineering/

I have seen Madicken teach and chair sessions and it's going to be awesome I want to goooooo! 😭😭😭😭

jni, 26 days ago to random

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, 1 month ago to random

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

jni, 1 month ago to random

“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, 1 month ago to random

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

jni, 3 months ago to mastodon

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, 3 months ago to SciPy2024

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, 3 months ago to random

@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, 3 months ago to random

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, 3 months ago to random

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, 3 months ago to random

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

jni, 4 months ago to random

The @pypi Trusted Publishers mechanism feels like magic. 🧙 Thank you to everyone who worked on it! 🤩 This page is slightly scary re the nitty gritty details but click on the quickstarts: so. Friggin. Simple. ❤️

https://docs.pypi.org/trusted-publishers/

jni, 4 months ago to random

@protonmail wow I have just logged in to my account after briefly playing with it back in 2015, and you guys have come a long way. 😍

I have a couple of Qs:

1. Is snooze coming to the mobile apps in the near future? I tend to snooze more when on mobile, not less.
2. Is there an API one could hook into to snooze emails? I basically want to snooze all emails in my inbox to random times in the next three months, so I don't get them all at once again.

Anyway, congrats on all the progress! ❤️🚀

jni, 5 months ago to random

This is great. I'm not that harsh on people that still post on X — loss is hard to accept. But please just prioritise posting here, even if it feels like you're not getting replies. It's a low-cost way to ensure that we don't give X (or any other corp that doesn't give a shit about us) a monopoly on our thoughts and discussion. Over time, we will build a community here.

https://www.xlast.org/

jni, 5 months ago to random

Absolutely loving these little API diagrams from the scikit-learn mooc. (https://inria.github.io/scikit-learn-mooc/)

It was also already worth the price of admission to see @GaelVaroquaux get handed some irises as a prop to explain the iris dataset! 🤣👏👏👏

A video capture of scikit-learn co-creator Gaël Varoquaux holding some irises. The slide title is "Why and when? Some examples of machine learning." Gaël is saying "Consider flowers, for instance. I'm not very good at recognising them." (The "iris" dataset is a very famous example in data science education, containing measurements of petals and sepals for various species of iris.)

jni, 5 months ago to random

Man web dev is so broken...

jni, 6 months ago to random

Any updates on the new open source licensing terms that Prusa was exploring in

https://blog.prusa3d.com/the-state-of-open-source-in-3d-printing-in-2023_76659/

?

If I want to buy an open source, forever repairable, hackable 3D printer today, is Prusa the best choice or…?

CC @stargirl

jni, 6 months ago to random

The @napari 0.4.19rc1 release candidate is now out on PyPI! You can install it with pip install -U --pre napari. Please help us put out the best release possible by trying it out! This is primarily a bug fix and maintenance release but there's still exciting stuff happening. Here's what you can expect:

• you can now install pydantic 2 in the same environment as napari. 🥳
• working with Labels is now much faster and more accurate thanks to an overhaul of how colours are mapped
  …
  1/2

jni, 7 months ago to random

Every now and then a kind soul upvotes an old answer of mine on SO, and it turns out to be a fun read years later. 😃

https://stackoverflow.com/q/62135639/224254

"For some reason, my mcp object didn't have an offsets attribute […] but searching the source code shows me that offsets is defined with the skimage.graph._mcp.make_offsets function. So I did a bad thing and imported from that private module, so I could claim what was rightfully mine — the offsets list […]"

Can we please start writing papers like this?

jni, 8 months ago to random

Reminder to turn on full text search for your posts in Preferences > Public Profile > Privacy and Reach > (Search section) > Include public posts in search results! This goes a long way towards making Mastodon interactions less ephemeral.

Screenshot of mastodon preferences UI showing "Public Profile" and "Privacy and reach" selected.

jni, 8 months ago to random

Whoo! CZI just announced round 6 of the Essential Open-source Software for Science (EOSS)! (Now jointly with the Kavli Foundation and the Wellcome Trust.) My favourite thing CZI does. If you write open source software used in science, check it out!

If you don't know, this is not a "propose a cool new software package" call — this gets at the heart of software sustainability and supports the boring stuff for established projects — maintenance, docs, onboarding, sprints…

https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/

jni, 8 months ago to scipy2023

Cool, my @SciPyConf @scipy2023 talk on @napari is up! 🥳 With great thanks to the organisers. 🙏❤️ Check it out here:

https://youtu.be/s362FTRzdg0

As a reminder, the repo and slides can be found here:

https://github.com/jni/napari-talk-scipy-2023

though you'll need to adapt it to use your own data to run much of it.

Finally, check out all the other amazing talks from the conf! Really looking forward to catching up with the tracks I missed (bc conflicts or frantically preparing for my own talk 😂)

https://www.youtube.com/@SciPy-Conf/videos

jni, 9 months ago to random

Looking at data in @napari is such a great way to quickly debug imaging code. Here I am learning that reading a dicom series is not as simple as stacking together the output of pydicom.dcmread().pixel_array. 😅 red: the above approach; grayscale: the napari-nibabel plugin.

Screenshot of a napari viewer with two layers in 2D slice view: a red one and a grayscale one. The objects in the slices are obviously misaligned.

jni, 9 months ago to random

It’s 2023 and Apple still hasn’t surpassed the 2002 iMac G4 design (the desk lamp). (And the commercial is still one of their best too!) https://www.theverge.com/23808948/imac-twenty-five-visual-history-apple-design-models

jni, 9 months ago to random

The Wobbly Table Theorem might be the most useful I know in everyday life. Works every time! (I guess that's the thing about theorems! 😂)

https://arxiv.org/abs/math/0511490

tldr: if your table is wobbly, rotate it around its central axis. At some point, as if by magic, all four feet will be firmly planted on the ground.

Amazingly, this theorem does not seem to have a Wikipedia page.