Marius Pachitariu
@marius10p
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running a lab @HHMIJanelia, data (neuro) scientist, visual cortex, large-scale recordings #Kilosort, #Suite2p, #Cellpose
Janelia Research Campus
Joined December 2011
Liked this story? Come work with us on the next one! Positions open:
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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🖥️ 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. 🔗 https://t.co/cwhj6ytIdA
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Cellpose3 from @marius10p and @computingnature uses deep learning to enhance degraded images for more accurate segmentation. https://t.co/ZkdIIELYbD
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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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We're back. Let's #AssembleForDemocracy. In the #ElectionEndgame, every vote counts 🗳️ #VoteBlue! Vote @KamalaHarris @Tim_Walz
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🖥️ Rastermap, a new visualization tool developed by the Stringer (@computingnature) & Pachitariu (@marius10p) labs, helps scientists uncover activity patterns in large-scale neural recordings. 🧠 🔗 https://t.co/31D8VsH7k4
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Read about our experience and that of others in building software for biology. #kilosort #suite2p #cellpose #facemap #rastermap
Six tips for going public with your lab’s software: https://t.co/Kc6svMnzZg 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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Six tips for going public with your lab’s software: https://t.co/Kc6svMnzZg 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
nature.com
Nature - It’s not enough to write high-quality programs. If you want to make your apps public — and usable — you should also follow these steps.
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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
https://t.co/vqzRDwXaE2
nature.com
Nature Neuroscience - Rastermap is an analysis method for exploring dynamical and spatial relationships among hundreds to hundreds of thousands of neurons. The algorithm uses a fast optimization...
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Make your next discovery using #Rastermap, a visualization method for large-scale neural data. Paper now out, w/ @marius10p : https://t.co/6cvInacEWV
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📢 #Rastermap paper out now, easily explore and visualize your neural recordings 🐭🐒🐟 and ANNs 🤖 https://t.co/UIzHDiGt5I. Updates from preprint include analyses of primate data and IBL task data. Video tutorial: https://t.co/6AyXSch52l
#Neuroscience #MachineLearning
Make your next discovery using #Rastermap, a visualization method for large-scale neural data. Paper now out, w/ @marius10p : https://t.co/6cvInacEWV
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#Kilosort and #Suite2p applied to human loop organoids. Great new work from @Sergiu_P_Pasca and team.
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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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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Reasons authors give for not sharing data when their paper says "data available upon request" https://t.co/OLrxgOLIlD
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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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Neat position at HHMI in Chevy Chase MD: "Open Science Strategy Program Coordinator" pay range $75-120k, PhD required https://t.co/lb8KtNKQbZ
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Work with us an AI scientist or engineer, apply now!
✨ 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 ➡️ https://t.co/uvV4wnML4D
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✨ 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 ➡️ https://t.co/uvV4wnML4D
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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 https://t.co/E6UZH8nn38
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https://t.co/QCtOIaybOj 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/
biorxiv.org
Advanced deep-learning methods, such as transformer-based foundation models, promise to learn representations of biology that can be employed to predict in silico the outcome of unseen experiments,...
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I’m excited to share the results of a massive collaborative effort from the @brody_lab, now in preprint form at: https://t.co/iom7m0B4jb Thread below:
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