lili

@lili@synapse.cafe

PhD in neuroscience
Right now focused on modeling 3D kinematics
Scientist at Allen institute of neural dynamics
She/her 🏳️‍⚧️ 🏳️‍🌈

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jonny, to random
@jonny@neuromatch.social avatar

The emerging field of Beethoven's Hair Studies is the only field where I try to keep up with the literature: https://doi.org/10.1093/clinchem/hvae054

lili,

@jonny "Furthermore, the Halm-Thayer Lock is one of the only 2 with an intact chain of custody; Beethoven hand-delivered the lock himself to the pianist Anton Halm in April 1826 (3)."

Did people in the 19th century just give each other locks of hair? Was this a common thing?

lili, to Neuroscience

I'm happy to present the last paper from my thesis!

Lisa Li and I set out to build a model of fly walking which is based on 3D kinematics data, handles perturbations, and includes sensorimotor delays. (This was supervised by Bing Brunton and @tuthill )

We set up a new modeling framework, generated fly walking with kinematics matched to real data, a simple metric for quantifying similarity of trajectories, and found constraints on delays for robust walking!

https://www.biorxiv.org/content/10.1101/2024.04.18.589965v1

#neuroscience #drosophila #walking #preprint

1/7

Model generates forward walking similar to real flies. Shown is an example comparison of real and simulated fly walking kinematics, visualized on a fly model by inverse kinematics (no further physics simulation).

lili, to Neuroscience

I've been working on a way to annotate in multiple views, with feedback for inconsistencies across views. There's still some way to go, but already it feels so cool after years of labeling only 2D views!
#neuroscience #annotation #PoseEstimation

lili, to chemistry

This paper is kinda wild:
https://pubs.acs.org/doi/10.1021/acscentsci.3c01593

"We have discovered that hard, electrical conductors (e.g., metals or graphite) can be adhered to soft, aqueous materials (e.g., hydrogels, fruit, or animal tissue) without the use of an adhesive. The adhesion is induced by a low DC electric field."

I can see this being quite useful for possibly attaching imaging equipment or electrodes for neural recordings.

lili,

A video demonstrating the electroadhesion technique

Video demonstrating reversible adhesion of graphite to AAm gel by by electroadhesion technique

jonny, to RSS
@jonny@neuromatch.social avatar

I guess this is turning into a real project so putting this out there if anyones interested:

We're making a very lightweight tool to create RSS feeds for journals from crossref metadata (with room for other sources). If ya dont know, many publishers are shutting down their RSS feeds to drive people onto their surveillance platforms, and every enshittification leaves behind an opening for adversarial interop.

This opens some interesting possibilities like creating feeds for keywords indexed across journals to start breaking down journals as the major organizational scheme of scholarly lit - papers have metadata keywords, but they mostly arent used, so lets use them!

Eventually wed like to write a FastAPI plugin similar to activitypub-express so we can make all feeds available on the fedi as well, and that would be a really nice set of tools to build for smaller AP projects that dont necessarily want to be full instances.

This is designed to be extremely deployable so you can run your own feed generator, but we'll also host a reference instance here at feeds.neuromatch.social once we get it running.

Just getting started, help wanted and welcome from anyone who loves #RSS and reading papers ♥

Repo: https://github.com/sneakers-the-rat/journal-rss

Cc @lili and @roaldarboel

Stems from this thread: https://neuromatch.social/@jonny/111668885237921256

lili,

@mpe @jonny @roaldarboel @gbilder

Thank you! I started looking into the feeds, and I found that some of the journals don't have up to date articles. For instance Physical Review D has no articles past 2015: https://api.crossref.org/journals/1550-7998/works

Do you know why that might be?

elduvelle, to random
@elduvelle@neuromatch.social avatar

What do people use nowadays as #RSSReaders? (Does the concept even still exist?)

It’s to keep track of relevant #ResearchPapers of interest as my main source used to be… Twitter and ResearchGate, which I’ll both be leaving before 2024

lili,

@jonny @elduvelle
I'm not sure what you mean about RSS feeds being bad? eLife has some great RSS feeds: https://elifesciences.org/alerts
Similarly for nature neuro ( https://www.nature.com/neuro/web-feeds ) or most journals. The trick is to look up "journal name rss" on your favorite search engine. Admittedly I only subscribe to the eLife ones, subscribing to science or nature anything is too much of a firehose for me.

You can follow any mastodon account with RSS.

For more broad science news, phys.org has some nice feeds that don't feel like firehoses: https://phys.org/feeds/

I follow a bunch of neuro blogs with RSS, but sadly most of them are defunct now... Still, I hope that we can come back to blogging!

lili, to academia

When going to academic talks, I've noticed that the more senior the academic, the less likely they are to take notes. I thought I would understand as I get older myself, but I still continue to take notes?

Has anyone else noticed this pattern?

If you've stopped (or started??) taking notes, then why?

#academia #notes

lili, to Neuroscience

Alright I defended my thesis! I'll be working at the Allen Institute for Neural Dynamics next. I will improve Anipose to make it even easier to set up 3D tracking for animals. I will also collect a large dataset of muscle dynamics & 3D kinematics on mice for building musculoskeletal models.

I'm excited to hang out in this space again. Will experiment with posting progress and thoughts on new papers here more often.

#neuroscience

lili,

@karihoffman

2 different labs have used Anipose to estimate 3D pose in marmosets!

https://doi.org/10.1016/j.cub.2023.05.032

https://doi.org/10.1242/jeb.243998

You may want to check out JARVIS as well: https://jarvis-mocap.github.io/jarvis-docs/#why-jarvis

It does work! I would like to make the process much simpler so labs can get to 3D pose data in a few weeks instead of a few months.

#neuroscience #monkey

tuthill, to Neuroscience

Congratulations to @lili on a superb PhD defense today!

Watercolor artwork by @lili's co-advisor Bing Brunton.

#neuroscience #phd

lili,

@jonny Thank you!! Yeah I've been working at UW with John and Bing. If you're ever in Seattle hit me up!

lili, to animals

What is the latest research in quantifying animal movement and behavior?

I wrote down a detailed overview here, based on what I saw at CVPR this year:
https://writings.lambdaloop.com/posts/cv4animals-2023/

WorldImagining, to mastodon French
@WorldImagining@mastodon.social avatar

#Mastodon functionality question:

When someone includes the url to a Mastodon post in a post (which people often do to stand in for "quote tweeting"), if I click on that url the post in question doesn't appear in the right-hand column of the web interface but instead opens a new tab from within the instance of that url. Worse, this means I'm not signed in there and can't directly engage with the post.

Possible to get these Masto urls to open within the web interface when clicked?

@Mastodon

lili,

@albertcardona @WorldImagining @Mastodon

I've been using the Mastodon simplified federation addon, and it solves exactly this problem:
https://github.com/rugk/mastodon-simplified-federation

lili, to Futurology

After thinking more and discussing with people here, synapse.cafe will defederate from any meta platform until further notice.

My main concerns are about monetization of our community, having to deal with corporate policing of our content, and potentially harassment from an influx of users.

Besides, as many others have mentioned, Meta has a bad record with regards to privacy and human rights, and there's no reason to expect their upcoming social platforms will be any different.

#meta #threads #admin

lili,

The main drawback of defederating is that people from this server won't be able to interact with people on Meta platforms (like threads).

I think it's worth the price. Many people (and indeed myself) have joined mastodon as an alternative to the corporate-owned social media, knowing that there is a smaller group of people here to interact with.

To federate with Meta is antithetical to the community ideals of the fediverse.

lili,

In full honesty, I am still figuring out what blocking Meta means in practice right now.

For now, I've suspended the server "threads.net". I'm not sure what else to do.

Do any other server admins know?

#server #admin #threads

lili, to Futurology

I'm still figuring out what to do about the meta threads coming in a few days. Reading and thinking more about it, I'm leaning more and more to signing the fedipact and committing to blocking or limiting meta servers.

I'm concerned about privacy issues, monetization of our community, "embrace and extend" issues, having to deal with corporate policing of our content, and potentially harassment from an influx of users.

I'm curious what people here think. Is there a reason I should hold off the decision or even go the other way?

#server #admin #meta #threads #fedipact

jameskelleher, to random

Titles of artworks are getting longer.

“After having declined in the first half of the twentieth century, use of long titles of ten words or more then picked up, growing from 1.0% of all titles of works created in the 1950s to 5.0% in the 2010s”

lili,

@jameskelleher What is entropy measuring here?

lili, to random

I'm having too much fun writing the acknowledgments section for my thesis. Help. It has already grown to 4 pages and I still have so many people to thank!

jonny, to random
@jonny@neuromatch.social avatar

anakin skywalker voice: now this is pettiness

lili,

@jonny was it banned on arxiv.org? why?

miturian, to random

Hi, since I'm brand new to Mastodon, I hope someone will answer a newbie question:
if I search in the search field top right (I'm in a browser and not on mobile), will I search other servers than synapse.cafe, or only this server?
Hope that made sense :)

lili,

@miturian Welcome! When searching, you'll see posts from all servers that synapse.cafe sees. Due to the distributed nature of mastodon, only some posts are visible. See this chart for details.

Searching by text on post content is broken in synapse.cafe right now, I'll fix it within a few days. Still, I've found that searching by hashtags to be a lot more reliable for exploring topics in mastodon and finding people to follow.

lili, to random

We made it! The server synapse.cafe is now on the joinmastodon.org page!

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