Marius Pachitariu (@marius10p)

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Marius Pachitariu@marius10p · Oct 2, 2020

Liked this story? Come work with us on the next one! Positions open: janelia.org/lab/pachitariu…

MMarius Pachitariu@marius10p · Apr 22, 2018

Story: 1. Neurons in the brain are very chatty: they fire action potentials, their basic unit of communication, even when there is nothing to communicate. For example in this video, in visual cortex recordings in complete darkness. Lots of chatting:

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HHMI | Janelia@HHMIJanelia · Feb 13

🖥️ A new version of #Cellpose – the popular tool developed by @computingnature & @marius10p that maps the boundaries of diverse cells in microscopy images – now works on less-than-perfect pictures that are noisy, blurry, or undersampled. 🔗janelia.org/news/newest-ve…

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Nature Methods@naturemethods · Feb 12

Cellpose3 from @marius10p and @computingnature uses deep learning to enhance degraded images for more accurate segmentation. nature.com/articles/s4159…

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Bill Madden@maddenifico · Nov 5

Rachel Maddow, imploring the agencies that protect the United States of America to wake the fuck up about the dangerous national security threat that is Elon Musk. 😳👇

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Mark Ruffalo@MarkRuffalo · Oct 31

We're back. Let's #AssembleForDemocracy. In the #ElectionEndgame, every vote counts 🗳️ #VoteBlue! Vote @KamalaHarris @Tim_Walz

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HHMI | Janelia@HHMIJanelia · Oct 24

🖥️ Rastermap, a new visualization tool developed by the Stringer (@computingnature) & Pachitariu (@marius10p) labs, helps scientists uncover activity patterns in large-scale neural recordings. 🧠 🔗janelia.org/news/new-tool-…

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Marius Pachitariu@marius10p · Oct 19

Read about our experience and that of others in building software for biology. #kilosort #suite2p #cellpose #facemap #rastermap

CCarsen Stringer @[email protected]@computingnature · Oct 18

Six tips for going public with your lab’s software: nature.com/articles/d4158… 1) make time for maintenance 2) simplify installation 3) add a GUI or good CLI 4) good documentation 5) use github/git 6) automated testing Any other tips people have? #OpenScience #OpenSource

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Carsen Stringer @[email protected]@computingnature · Oct 18

Six tips for going public with your lab’s software: nature.com/articles/d4158… 1) make time for maintenance 2) simplify installation 3) add a GUI or good CLI 4) good documentation 5) use github/git 6) automated testing Any other tips people have? #OpenScience #OpenSource

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Nature Neuroscience@NatureNeuro · Oct 18

Rastermap: a visualization method that displays large-scale neural data (even hundreds of thousands of neurons) as a raster plot after sorting them along a one-dimensional axis based on their activity patterns @computingnature @marius10p @HHMIJanelia nature.com/articles/s4159…

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Carsen Stringer @[email protected]@computingnature · Jul 29, 2023

Make your next discovery using #Rastermap, a visualization method for large-scale neural data. Paper now out, w/ @marius10p : biorxiv.org/content/10.110…

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Marius Pachitariu@marius10p · Oct 16

📢 #Rastermap paper out now, easily explore and visualize your neural recordings 🐭🐒🐟 and ANNs 🤖 nature.com/articles/s4159…. Updates from preprint include analyses of primate data and IBL task data. Video tutorial: youtu.be/oQHq7yUWn2k #Neuroscience #MachineLearning

CCarsen Stringer @[email protected]@computingnature · Jul 29, 2023

Make your next discovery using #Rastermap, a visualization method for large-scale neural data. Paper now out, w/ @marius10p : biorxiv.org/content/10.110…

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Marius Pachitariu@marius10p · Oct 16

#Kilosort and #Suite2p applied to human loop organoids. Great new work from @Sergiu_P_Pasca and team.

SSergiu P. Pasca@Sergiu_P_Pasca · Oct 15

Today we introduce human neural loop #assembloids created from 4 parts derived from stem cells to study the cortico-striato-midbrain-thalamo-cortical pathway and to model neurodevelopmental disease Work led by the remarkable Ji-Il Kim and Yuki Miura in the lab. Also in…

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Sergiu P. Pasca@Sergiu_P_Pasca · Oct 15

Today we introduce human neural loop #assembloids created from 4 parts derived from stem cells to study the cortico-striato-midbrain-thalamo-cortical pathway and to model neurodevelopmental disease Work led by the remarkable Ji-Il Kim and Yuki Miura in the lab. Also in…

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Science of Science @ AOM@MishaTeplitskiy · Oct 10

Reasons authors give for not sharing data when their paper says "data available upon request" nature.com/articles/s4159…

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Angeline J. Dukes, PhD@TheRealDrDukes · Oct 7

Now that I have some time, let me tell y’all about the DISRESPECT that Black In Neuro experienced by SfN staff last night 🤬 We did an #SfN24 “sponsored social” and I am livid with how we were treated. I don’t care what you say to me, but you will NOT disrespect my team.

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Anne Carpenter, PhD@DrAnneCarpenter · Sep 28

Neat position at HHMI in Chevy Chase MD: "Open Science Strategy Program Coordinator" pay range $75-120k, PhD required hhmi.wd1.myworkdayjobs.com/External/job/H…

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Marius Pachitariu@marius10p · Sep 27

Work with us an AI scientist or engineer, apply now!

HHHMI | Janelia@HHMIJanelia · Sep 25

✨ We’re excited to announce that we’re recruiting scientists for AI@HHMI, our new $500 million initiative to embed AI systems throughout every stage of the scientific process. 🖥️ 🔗 Check out the first of our open positions & apply today ➡️ai.hhmi.org/#join-our-team

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HHMI | Janelia@HHMIJanelia · Sep 25

✨ We’re excited to announce that we’re recruiting scientists for AI@HHMI, our new $500 million initiative to embed AI systems throughout every stage of the scientific process. 🖥️ 🔗 Check out the first of our open positions & apply today ➡️ai.hhmi.org/#join-our-team

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HHMI | Janelia@HHMIJanelia · Sep 24

Atika Syeda (@Atika_Ibrahim) is a graduate scholar in the Stringer (@computingnature) & Pachitariu (@marius10p) labs @hhmijanelia where she uses machine learning to better understand the relationship between behavior & sensory information in mice. 🧵1/10 janelia.org/people/atika-i…

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Anshul Kundaje (anshulkundaje@bluesky)@anshulkundaje · Sep 21

biorxiv.org/content/10.110… Nice benchmark of single cell "foundation models" (scGPT, scFoundation) and GEARS (a GNN model) further hyped as "virtual cell models" against linear baselines on perturbation prediction. Long-story short: they can't beat the linear baselines. 1/

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Julie Charlton@julie_charlton_ · Aug 23

I’m excited to share the results of a massive collaborative effort from the @brody_lab, now in preprint form at: tinyurl.com/crs85sta Thread below:

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