running a lab @HHMIJanelia, data (neuro) scientist, visual cortex, large-scale recordings #Kilosort, #Suite2p, #Cellpose
Janelia Research Campus
Joined December 2011
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Liked this story? Come work with us on the next one! Positions open: janelia.org/lab/pachitariu-l…
Marius Pachitariu retweeted
🖥️ 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-vers…
Marius Pachitariu retweeted
Cellpose3 from @marius10p and @computingnature uses deep learning to enhance degraded images for more accurate segmentation. nature.com/articles/s41592-0…
Marius Pachitariu retweeted
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. 😳👇
Marius Pachitariu retweeted
We're back. Let's #AssembleForDemocracy. In the #ElectionEndgame, every vote counts 🗳️ #VoteBlue! Vote @KamalaHarris @Tim_Walz
Marius Pachitariu retweeted
🖥️ 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-he…
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: nature.com/articles/d41586-0…
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
Marius Pachitariu retweeted
Six tips for going public with your lab’s software: nature.com/articles/d41586-0…
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
Marius Pachitariu retweeted
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/s41593-0…
Marius Pachitariu retweeted
Make your next discovery using #Rastermap, a visualization method for large-scale neural data. Paper now out, w/ @marius10p : biorxiv.org/content/10.1101/…
Marius Pachitariu retweeted
📢 #Rastermap paper out now, easily explore and visualize your neural recordings 🐭🐒🐟 and ANNs 🤖 nature.com/articles/s41593-0…. Updates from preprint include analyses of primate data and IBL task data.
Video tutorial: youtu.be/oQHq7yUWn2k #Neuroscience #MachineLearning
Make your next discovery using #Rastermap, a visualization method for large-scale neural data. Paper now out, w/ @marius10p : biorxiv.org/content/10.1101/…
#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 collaboration with the @marius10p lab at @HHMIJanelia
Video shows a four-part neural assembloid displaying emergent synchronized activity after a couple of hundred days of integration
Marius Pachitariu retweeted
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 collaboration with the @marius10p lab at @HHMIJanelia
Video shows a four-part neural assembloid displaying emergent synchronized activity after a couple of hundred days of integration
Marius Pachitariu retweeted
Reasons authors give for not sharing data when their paper says "data available upon request"
nature.com/articles/s41597-0…
Marius Pachitariu retweeted
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.
Marius Pachitariu retweeted
Neat position at HHMI in Chevy Chase MD:
"Open Science Strategy Program Coordinator"
pay range $75-120k, PhD required
hhmi.wd1.myworkdayjobs.com/E…
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 ➡️ai.hhmi.org/#join-our-team
Marius Pachitariu retweeted
✨ 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
Marius Pachitariu retweeted
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-ibr…
Marius Pachitariu retweeted
biorxiv.org/content/10.1101/…
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/
Marius Pachitariu retweeted
I’m excited to share the results of a massive collaborative effort from the @brody_lab, now in preprint form at: tinyurl.com/crs85sta
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