@computingnature

group leader @HHMIJanelia | diversity + open-science for better science | she/her | VOTE BLUE Mostly on MASTODON: @Computingnature@neuromatch.social, join us!

 Ashburn, VA
mouseland.github.io/
Joined June 2016
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The first preprint of my postdoc with @jtdudman is now online! Here we wanted to understand the algorithms mice use when learning to forage in large environments with many potential resources. 1/n biorxiv.org/content/10.1101/…
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Amazing talk about imaging and discovering C. elegans embryogenesis by Hari Shroff from @HHMIJanelia presenting at #I2K2024
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It's great to be at #I2K2024 #i2k and see (almost) everyone in bioimage analysis. If you're interested in OME-Zarrs or what we're doing with Fractal, stop by my poster today! :)
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#I2K is in full swing! Had a great time presenting my poster yesterday. Excited for what’s next! ✨ #I2K2024
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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. 🧠 🔗janelia.org/news/new-tool-he…
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We performed ephys recordings, in head-fixed and freely moving animals, and found the head-direction system boosts its gain when a landmark is seen—suggesting a mechanism that signals stronger confidence in vision when natural objects are present. 4/
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👆 good use case examples/tutorials help a lot!
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Guidance for implement on HPC. Colab demo notebook. Suggestions on data size limitation.
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Great tips! We’ve been through this with @thepynapple, to do it properly is much harder than you can imagine.
Carsen Stringer @[email protected]@computingnature18 Oct 2024
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
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Video tutorials like your for using Cellpose
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We are excited to introduce PetaKit5D, a comprehensive suite of software tools designed to tackle challenges in the handling of large datasets and make processing of petabyte-scale datasets feasible: nature.com/articles/s41592-0…
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This is a *beautiful* paper and method, and while the paper itself is very careful about drawing conclusions from the variety of datasets it analyzes, I'd say the edifice of "the brain is chaotic" hypothesis is crumbling!
Carsen Stringer @[email protected]@computingnature16 Oct 2024
📢 #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
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Wonderful tool for exploring neural data! Stationary and dynamic patterns, all in one place and along a single dimension. Not a petri dish mold-shaped point-cloud in sight. It’s become one of my favorite ways of trying to guess at what neurons are up to.
Carsen Stringer @[email protected]@computingnature29 Jul 2023
Make your next discovery using #Rastermap, a visualization method for large-scale neural data. Paper now out, w/ @marius10p : biorxiv.org/content/10.1101/…
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It's the middle of breast cancer awareness month! I must admit I dislike getting mammograms. It's not the procedure, it's just the fear of the unknown. But, breast cancer can be very treatable if caught early, so please get checked!
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@KordingLab and I efficiently optimize high-dimensional biophysical neuron models with heterogeneous active dendrites using the gradient-based backpropagation of error algorithm typically used to train models in deep learning. Preprint on arxiv: arxiv.org/abs/2407.04025 1/18
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🚨Preprint‼️ 1/ Predicting neural activity is notoriously difficult and requires complicated models. Here we develop simple “minimodels” which explain 70% of neural variance in V1! 🐭🐒 #neuroai @computingnature @marius10p @NunezKant Paper: biorxiv.org/content/10.1101/… Recording 🔬 :
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Excited to share our new preprint on spatial single-cell analysis of human cortical development! We used #MERFISH to analyze 16 million cells, revealing surprisingly early prenatal specification of human cortical layers and areas. (1/11) #Neuroscience biorxiv.org/content/10.1101/…

Spatial Single-cell Analysis Decodes Cortical Layer and Area Specification

The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas1,2. The layers and areas are distinguished both...

biorxiv.org
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The mentoring experience is one of the most unique assets of the academy, for both the students and the mentors. So if you are at a stage of your (academic or not) career and feel like you have two to three hours in all of July to spare, become a mentor yourself
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These results seem compelling. But regardless of benchmarking results, Cellpose absolutely is SOTA for diverse applications in the hands of real users and 2nd place isn’t close.
Carsen Stringer @[email protected]@computingnature7 Apr 2024
#Cellpose remains the state-of-the-art for cellular segmentation. See our new paper, in response to Ma et al, Nat Methods 2024. Paper: biorxiv.org/content/10.1101/… Leaderboard results ⬇️⬇️⬇️
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Excited to share my PhD work in @pgolshani 's lab designing and building low-cost miniature 2P microscopes with everyone! They cost < $10k USD (even at low production runs), are fitted with 2 on-board SiPM detectors, and are completely open-source! 1/5 biorxiv.org/content/10.1101/…
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