@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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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

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

brettcannon, to random
@brettcannon@fosstodon.org avatar

As a reminder, you pay for open source w/ kindness. Don't make demands (you can request), argue (you can have a pleasant conversation), or be mean (you can always just not say anything). Otherwise your "refund" for that open source you apparently "overpaid" for could consist of being called out for your behaviour, ignored, blocked, the OSS contributor walking away/burning out, or that code you were using being yanked off the internet.

https://snarky.ca/setting-expectations-for-open-source-participation/

jni,
@jni@fosstodon.org avatar

@brettcannon there was this long-running PR that I was quite excited about — I’d even paired with the contributor a few times. But it lost steam right near the end, as I couldn’t find time for a deeper review. Then the contributor wrote “I find it frankly incredible that it’s been almost a year and this hasn’t been merged.”

afaik that’s the last comment on that PR, now years later. Not out of malice or pettiness — I just can’t bring myself to open it again, and there’s always other priorities.

mkennedy, to random
@mkennedy@fosstodon.org avatar

I just published a brand new package to PyPI:

Umami Analytics - An API Client for Python

Umami is excellent. Works amazing and is an open-source, privacy-focused platform that replaces Google Analytics, Plausible-IO, etc.

https://github.com/mikeckennedy/umami-python

It’s been a busy week for infrastructure at @talkpython. More to come in this space soon.

jni,
@jni@fosstodon.org avatar

@mkennedy @talkpython what are some of the benefits of umami vs plausible? (A quick browse of the home page makes them look ~identical…)

jni,
@jni@fosstodon.org avatar

@mkennedy @talkpython good questions, I have no need for those things so I don’t know, but they are certainly plausible (heh) differentiators for umami. 😃 but not a reason for me to migrate my existing sites (yet). Thanks!

iris, to random
@iris@neuromatch.social avatar

It’s the nature of grant-funded research, but it still sucks — my current funding is ending, new funding is not a certainty, and I am therefore on the job market.

I’m interested in writing software to support science. My PhD-level expertise is in computational methods development for structural biology (X-ray crystallography and cryoEM), and I have some experience in several areas further afield (math, phys, CS, chem, bio). I have HPC (Slurm, SGE and LSF) and GPU experience, 11 years of python and bash, lots of scripting, automation, and parallel computing, and a smaller amount of a bunch of other stuff. Plus I’m a quick learner and love a challenge.

I’d love to stay in the Bay Area if I can, but will consider any other major cities, US or further, that are safe for trans people. Seattle and Boston are already on the radar.

Any recommendations, tips, or general advice is appreciated!

P.S. for the 2-3 months I’m likely to be between jobs, I would be thrilled to do a short gig assisting on a research vessel at sea — definitely shoot me any news of those!

jni,
@jni@fosstodon.org avatar

@iris in the Bay Area the CZ Institute for Advanced Biological Imaging (or Chan Zuckerberg Imaging Institute, I can't figure out their branding 😂) looks like a great fit. They have open positions for a data integration engineer and a machine learning for CryoET engineer, and I'm pretty sure they'd open more positions for the right person:

https://www.czimaginginstitute.org/careers/

vicgrinberg, to random
@vicgrinberg@mastodon.social avatar

Last hours in Malaga... On to Madrid & work!

jni,
@jni@fosstodon.org avatar

@vicgrinberg oh! Then try the churros at San Ginés in the old town! Those are proper! 😂🤤 (and imho the best in town.)

jni, to random
@jni@fosstodon.org avatar

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/

kisharrington, to random
@kisharrington@mastodon.social avatar

Playing with an adaptation of the processing code here (https://twitter.com/hisadan/status/1697878658437054785?s=20) to napari.
Tooted from with .

jni,
@jni@fosstodon.org avatar

@kisharrington cool but after seeing the tweet I am disappointed not to see a slider. 😜 (plus it might look quite spectacular as a kymograph)

vicgrinberg, to spain
@vicgrinberg@mastodon.social avatar

The perfect breakfast in Spain before a 15km walk.

jni,
@jni@fosstodon.org avatar

@vicgrinberg where are you? Those are not the churros I know and love and indeed I have never encountered such a thing.

jni, to random
@jni@fosstodon.org avatar

@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,
@jni@fosstodon.org avatar

@protonmail don't have or don't yet have a public-facing API? 😭🙏 I just noticed that you have a Python client so having a snooze API accessible from the Python client would immediately move me to Proton. 😊

philiphubbard, to Neuroscience
@philiphubbard@fediscience.org avatar

The neuVid system for #Neuroscience / #CellBiology videos now supports #GenerativeAI. Given natural language, it makes a video with #Blender (#Blender3D). E.g.:

"Frame on neuron 393766777 from the Janelia hemibrain. Orbit the camera 45 degrees over 6 seconds, and move in 25% while orbiting. 1 second in, fade on neuron 1196854070 over 1 second. Then fade on the output synapses of 393766777 connecting to 1196854070 taking 1 second. Synapses should be extra big."

https://github.com/connectome-neuprint/neuVid

(1/3)

A video of two neurons from the Janelia FlyEM hemibrain data set and the synapses connecting them.

jni,
@jni@fosstodon.org avatar

@kristinmbranson @philiphubbard agreed, fantastic stuff. I think this sort of thing is a nice sweet spot for LLMs — stuff that would be quite tedious to do even for an expert.

jni, to random
@jni@fosstodon.org avatar

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/

DrBiscuit, to academicchatter French

I truly do not know what to think about this situation and I would love having your thoughts on this @academicchatter
One of my papers was accepted to be published in July (after the 2nd round of reviews, 1st round was minor modifications), announced on the website, I was asked whether I wanted to buy the pinted copy of the journal etc. My co-author and I were asked to do some modifications over a 1 week period. We were off at the time and asked for a delay that was accepted. (1/...)

jni,
@jni@fosstodon.org avatar

@DrBiscuit @GeorgKrammer @mikagratzke @academicchatter even with that situation, I would suggest your co-author explains the situation to her employer (if she needs to bring it up at all), since you have clear evidence of every step. I’ve never heard of such a thing and imho not only should you pull out you should name the journal to warn the rest of us to never publish there. Astounding.

Whatever you do, best of luck, hard to read about this. 💔

jni, to Pixelfed
@jni@fosstodon.org avatar

Hi users! My Flickr Pro subscription came up for renewal, and now I know I can do better! 😃 Any tips for choosing a server? I see most servers have a per-photo storage size limit (15MB), but are there limits on bandwidth/total number of photos? Can pixelfed be used for private/semi-private photos ("Anyone with the link can view" kind of situations)?

jni,
@jni@fosstodon.org avatar

lol

albertcardona, to infosec
@albertcardona@mathstodon.xyz avatar

Hi community: any recommended practices for preventing a personal blog webpage from being dominated by crawlers?

The robots.txt seems largely ignored. Crawlers presently consume ~75% of resources according to the access logs.

I don't mind not being listed on any web search engines.

Would a basic auth work? Can one make the basic auth dialog show a message that provides the password hint in it, like "What is my first name?"

jni,
@jni@fosstodon.org avatar

@albertcardona @giorgiogilestro

Neither Amazon nor (in my case) GitHub care, but so what? You own the domain and you (presumably) have a local backup? If they decide to change cost model/lock you out/whatever shenanigans, you can always move? For a static site I don’t know why you wouldn’t use gh-pages these days… Again, not in love with GH, it’s just very easy and has no lock-in.

jni,
@jni@fosstodon.org avatar

@albertcardona @giorgiogilestro but you haven’t explained why you need a VM for a simple static site, as opposed to it being a liability. To me, that you’re considering putting an annoying prompt in front of every page suggests that it’s not worth the trouble. Or…?

jni,
@jni@fosstodon.org avatar

@albertcardona @giorgiogilestro I feel like your writings should have more reach than that. 😊

jni, to random
@jni@fosstodon.org avatar

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, to random
@jni@fosstodon.org avatar

Man web dev is so broken...

kisharrington, to random
@kisharrington@mastodon.social avatar

The desire to take a week off just so you can focus on a work task for multiple days without needing to context switch.

jni,
@jni@fosstodon.org avatar

@kisharrington lowkey maybe we should. Some key parts of napari were written by @royerlab and me at an Airbnb by the beach out here. We can probably finish your PR in a week (and with a high level of polish).

kisharrington, (edited ) to random
@kisharrington@mastodon.social avatar

I'm hiring a Software Engineer to work on ML for CryoET at the new CZ Imaging Institute in Redwood City, CA: https://grnh.se/8394d0275us

We're building a fantastic team at CZII. We have a supportive group of folks in a flat org structure and are all working hard to accelerate the future of imaging. The person who takes this position will have space for creativity and collaboration. I look forward to meeting you if I haven't already :)

jni,
@jni@fosstodon.org avatar

@kisharrington I’ve seen people use the tag for job ads.

yetiinabox, to random
@yetiinabox@todon.nl avatar

Unsurprisingly, Science published an attack on academic unions. It portrays successful struggles to improve pay and conditions for PhD and postdocs as anti-individualist (!) and an attack on innocent research group leaders.

https://www.science.org/content/article/student-and-postdoc-unions-proliferate-academia-scrambling-adapt

Among other gems:

'Individual faculty members, who support grad student researchers and postdocs out of their own grants, are having to take a careful look at their budgets as well. “Every lab is in many ways its own little microbusiness,” says Lisa García Bedolla, vice provost for graduate studies and dean of the graduate division at UC Berkeley. '

and

'“less research is going to be produced per dollar of [grant] money,” Nestler says. "This is the way the … research enterprise will have to change.”'

jni,
@jni@fosstodon.org avatar

@jonny @yetiinabox this hits hard today, we had a town hall on research assessment at Monash Fac. of Med. Highlight was that individual article metrics were inadmissible because we must use internal Monash data, which comes from Elsevier Pure, which (shockingly) emphasises journal metrics. We use a thing called “Cumulative Impact Factor” I shit you not.

Faculty head didn’t love it but had a “my hands are tied” attitude. And I’m like how can this possibly be??? How can we be so powerless???

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