computingnature

@computingnature@neuromatch.social

group leader @ HHMIJanelia, thinking about thinking, 🔬#suite2p #cellpose #facemap #rastermap | diversity and open-science for better science | Ⓥ | she/her

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computingnature, to python

Spike sorting with #Kilosort in #python w/ #pytorch + @pyqtgraph !
>>> pip install kilosort[gui]

To learn more, check out the paper (https://www.nature.com/articles/s41592-024-02232-7), the docs (https://kilosort.readthedocs.io/en/latest/ by Jacob Pennington), or watch the talk (https://youtube.com/watch?v=LTSmoACr918 by @marius10p )
#neuroscience

computingnature, to bioinformatics

Despite all their hype in AI, we found that Transformers do not outperform for cellular segmentation tasks: https://www.biorxiv.org/content/10.1101/2024.04.06.587952v1

Cellpose outperforms winner of Neurips challenge (Ma et al 2024) on test set images. We show example images from the test set with Cellpose segmentations overlaid in yellow.

computingnature,

@albertcardona :) the challenge authors updated the test set since the challenge so we had to submit our masks and the winning team's masks to get the scores.

The winning Mediar team used the Cellpose flow approach (our code) and used a transformer instead of a CNN for prediction. On this dataset, it doesn't seem like the transformer improves performance. We also tested transformers on an even larger dataset and did not find a performance boost (blue and black curves) (from https://www.biorxiv.org/content/10.1101/2024.02.10.579780v2):

computingnature, to Neuroscience

"Artificial intelligence brings a virtual fly to life" ! #neuroscience #MachineLearning
https://www.janelia.org/news/artificial-intelligence-brings-a-virtual-fly-to-life , congrats Roman, @srinituraga @kristinmbranson et al

simulated fruit fly flying

computingnature, to random

Check out our lab’s recent work on visual learning and representations at the workshops:

computingnature, to Neuroscience

"A combinatorial code of action and context for motor memory." Jae-Hyun Kim, Kayvon Daie, Nuo Li. Really nice talk, context-specific codes in continual learning, and no representational drift observed in ALM https://www.youtube.com/live/Kq5f36OwFKU?feature=shared

brembs, to Neuroscience
@brembs@mastodon.social avatar

Some interesting !
When flies like sit, walk or fly, the gain in their motion vision adapts:
https://journals.biologists.com/jeb/article/217/10/1737/14000/Octopaminergic-modulation-of-the-visual-flight
https://www.nature.com/articles/nn.2492
https://www.jneurosci.org/content/31/25/9231
Like many other animals, flies also attenuate expected motion input during turns:
https://www.sciencedirect.com/science/article/pii/S0092867416316798?via%3Dihub
https://www.sciencedirect.com/science/article/pii/S0960982221013361?via%3Dihub
https://www.nature.com/articles/nn.4083
Because mice appear to have similar features, this was considered quite general.
Work in monkeys now challenges that notion:
https://www.thetransmitter.org/animal-models/monkey-studies-throw-wrench-into-decade-old-idea-about-movements-effect-on-visual-cortex/

computingnature,

@brembs @NicoleCRust @albertcardona @PessoaBrain FYI in mice and zebrafish, spontaneous (movement-driven) and stimulus-driven patterns are largely orthogonal, so high-fidelity and high-dimensional visual representations still exist in mouse visual cortex that the mouse can and does use to do complex visual behaviors. I would agree with @NicoleCRust that mouse V1 is more of an association area than in primates, and this association still has to happen somewhere in primates, so hopefully insights from mice can still be useful in that context. (Our paper: https://www.science.org/doi/10.1126/science.aav7893; review: https://www.sciencedirect.com/science/article/pii/S0896627322005888)

NicoleCRust, to random
@NicoleCRust@neuromatch.social avatar

Ugh.

https://www.vulture.com/article/hugo-awards-china-censorship-controversy.html

the volunteer body that administered the 2023 Hugo Awards appeared to have directly engaged in self-censoring the nominees over political concerns about the host country, China. The emails allege members of the Hugo administration team succeeded in keeping certain books off-ballot because they wanted to operate under Chinese laws related to content and censorship

computingnature,

@NicoleCRust oh no :( I recently read Babel (it was very good!)

“I wish to clarify that no reason for Babel’s ineligibility was given to me or my team. I did not decline a nomination, as no nomination was offered … I assume this was a matter of undesirability rather than ineligibility.” (https://www.theguardian.com/books/2024/jan/24/science-fiction-awards-held-in-china-under-fire-for-excluding-authors)

computingnature, to random

Applications open for freeman hrabowski scholars program for early career researchers #hhmi https://www.hhmi.org/news/hhmi-opens-national-competition-freeman-hrabowski-scholars-program

computingnature, to random

#Cellpose 3! Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p https://www.biorxiv.org/content/10.1101/2024.02.10.579780v1

(click to play gif)

noisy images are denoised by a deep learning algorithm to improve segmentation, then segmented by another deep learning algorithm

thetransmitter, to random
@thetransmitter@mastodon.social avatar

We’re just one day away from International Day of Women and Girls in Science. Is there a woman who inspired you to pursue a career in neuroscience?

Tag her or share your story below.

computingnature,

@NicoleCRust @thetransmitter I remember seeing Adrienne speak at the first cosyne I went to and it was an awesome and inspiring talk, it got me really excited about spontaneous activity.

I also remember early in grad school reading Kanaka Rajan's paper about eigenspectra of random neural networks, and being really inspired by it. I was working on spiking neural networks at the time, and there were very few women working in that area. (https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.97.188104)

jonny, to random
@jonny@neuromatch.social avatar

Ok im procrastinating doing a hard thing, who has got a really nice shell/editor setup they want to brag about? Im always interested in all the little hidden ways ppl make nests on their computers

computingnature,

@jonny WHAT how did I not know this? (I mostly used emacs in grad school, and those are the same in emacs!) now I use VScode for most things

computingnature, to Neuroscience

Simultaneous, cortex-wide and cellular-resolution neuronal population dynamics reveal an unbounded scaling of dimensionality with neuron number
https://www.biorxiv.org/content/10.1101/2024.01.15.575721v1

#neuroscience #dimensionality

computingnature, to Neuroscience

Check out this great new study led by Katie Schretter, investigating fighting female fruit flies -- who headbutt, shove & fence each other to guard prime egg-laying territory -- to ultimately better understand aggressive behavior in humans. https://www.janelia.org/news/fighting-fruit-flies-help-researchers-understand-why-we-stay-angry #neuroscience #drosophila

two female flies fighting!

computingnature, to science

AI under the microscope: the algorithms powering the search for cells: https://go.nature.com/3SVdFur. Nice article by Michael Eisenstein about cellular segmentation, with a shout out to #cellpose :) #biology #deeplearning

computingnature, to random

Neural activity across cortex is high-dimensional and ... complicated. Still, those fine neural features can be predicted from orofacial behaviors in mice! Great work by Atika Syeda et al in the lab!

Try out the all-new keypoint-based #facemap, paper here: https://www.nature.com/articles/s41593-023-01490-6

computingnature,

Play gif to check out the 🐭 orofacial movements!

Code: https://github.com/mouseland/facemap
Data: https://janelia.figshare.com/articles/dataset/Facemap_a_framework_for_modeling_neural_activity_based_on_orofacial_tracking/23712957

mouse face with keypoints tracked

computingnature,

If you're interested, there's also a summary of the paper by Nanci Bompey here, about reading the mouse mind from its face: https://www.janelia.org/news/reading-the-mouse-mind-from-its-face-new-tool-decodes-neural-activity-using-facial-movements

computingnature,

@jonny thanks we used a convolutional neural network to predict neural activity from the keypoints (fyi the figure is showing test data, our train / test periods are 10 min / 3.5 min long to avoid anything mischievous).... why these behavioral representations are brainwide is a really good question we still don't know the answer to

computingnature,

@jonny nice, not sure if it will work on this data but yes we shared all the raw movies :) we find that ellipse fitting is the most robust method when the pupil is a bit smaller, we also tried training a u-net to segment it and it didn't perform better

computingnature,

@NicoleCRust thanks!

computingnature, to news

Our lab is presenting at #SfN23 #SfN2023 see all presentation times here! https://mouseland.github.io/#news

Sun AM and Tues PM we will have stickers and pins for anyone who visits the posters #opensource

computingnature,

all presentations from the lab, exploring behavioral and visual responses in cortex: #SfN23 #SfN2023

computingnature,

also we are hiring postdocs, please get in touch if you're interested and I'll come by your poster! and/or say hi Sun AM. #SfN23 #SfN2023

jonny, (edited ) to random
@jonny@neuromatch.social avatar

This post will serve as the fediverse representation of my poster for #SfN23 :

Social-First #P2P: Strategies for Joy, Agency, and Ethics in Digital Infrastructure.
main website: https://jon-e.net/sfn23/
conference page: https://www.abstractsonline.com/pp8/#!/10892/presentation/35685
PSTR241.22 / WW65
November 13, 2023, 8:00 AM - 12:00 PM
WCC Halls A-C

This post is linked to the poster's website, https://jon-e.net/sfn23/ which embeds comments beneath this post. Comments below here serve as a discussion for those that can't be at the conference, or otherwise want to mark up the work.

edit 23-11-17: Added alt text, references, brief descriptions of related projects.

computingnature,

@jonny "if our wildest dreams for "open science" are to pay amazon to rent our own data... we need better dreams" 💯 there is this weird push for expensive (and carbon-unfriendly) cloud hosting of raw data in neuroscience. everything else on the poster is also awesome.

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