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Jonna Singh

@jonnasingh.bsky.social
758 followers 503 following 97 posts

Interoception, psychedelics, pain, flashy neurons, and everything in between prev basal ganglia and birds Postdoc @ Andermann lab

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Jonna Singh @jonnasingh.bsky.social · 27/08/2026
Congrats Matt! Super cool. But also, [School rules!] was right there
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
10/ Link to paper: www.biorxiv.org/content/10.6... EASI-PASS: github.com/orena1/easi-...
biorxiv.org
EASI-PASS: An accessible pipeline for linking functional imaging and mRNA profiling
We developed EASI-PASS, a reliable, high-throughput method for estimating the molecular identity of functionally characterized cells by merging live imaging with subsequent fixed-tissue imaging using ...
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
9/ This was a very fun team lift, shoutouts to Josh, Crystian, Oren, Bettina, Sarah, and Ana who made critical contributions, and @markandermann.bsky.social for letting this side project evolve! Be on the lookout for EASI-PASS applications on everything from interoception to memory!
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
8/ We hope this is a useful resource for labs interested in bridging across genes and function. We're particularly interested in getting and implementing feedback, so please feel free to send us any comments.
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
8/ We wanted EASI-PASS to be easy to pick up, and fully end-to-end. Starts with your tiffs, includes modules for segmentation, mRNA alignment, signal extraction, cell matching (including Soma-print, a great new algorithm from the Schnitzer lab), and outputs one table with all relevant info.
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
7/ In acute brainstem slices, we found a marker for spinorecipient neurons important for chronic pain. Our imaging prep also allowed us to ask whether inputs were likely to recruit specific cell types at the local (<50 um) scale w/ @crystianmassengill.bsky.social, @praneelsunkavalli.bsky.social
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
6/ In cortex, we found large scale cell-type specific differences in the spatial structure of correlated activity led by Josh Stern + Sarah Cook
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
5/ We applied EASI-PASS to acute brainstem slice imaging and in vivo cortical imaging data. In total, we matched around 40,000 cells, averaging around 3000 per sample (~80% match rate)
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
4/ EASI-FISH is a protocol for iterative mRNA labeling in cleared, expanded *thick* tissue. While not required, we found that EASI-FISH is readily adoptable, and is a nice way to preserve 2P imaged planes in a single tissue sample EASI-FISH: pubmed.ncbi.nlm.nih.gov/34875226/
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
3/ Thus, EASI-PASS was created! EASI-PASS (EASI-FISH Post-hoc Alignment by Spatial Segmentation) uses segmented cell masks to guide 2P to post-hoc mRNA alignment. EASI-PASS matched ~40k neurons, is computationally cheap, scalable, and can be used with any pair of segmented images
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
2/ Our goal was to make an accessible, practical method that would allow more labs to measure neuronal activity and mRNA in the same neurons. Something easy to use, self-contained, and compatible with standard microscopes (confocals/2Ps)
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Jonna Singh @jonnasingh.bsky.social · 26/08/2026
We're excited to present EASI-PASS! We can record the activity of many neurons, and separately, the expression of many genes. A natural next step for the field is to link these two types of information. 🧵👇 1/n
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Kanaka Rajan @kanakarajanphd.bsky.social · 07/08/2026
(1/8) Our approach for untangling brain-wide interactions is out today in @cp-neuron.bsky.social! Current-Based Decomposition (CURBD) uses RNNs constrained by real neural data to reveal the input driving neurons, uncovering how brain regions talk to each other. doi.org/10.1016/j.ne... 🧵👇
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Jonna Singh @jonnasingh.bsky.social · 27/07/2026
Favorite way to browse Bsky (:
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Lorenzo Posani @lorenzoposani.com · 15/07/2026
Out today on @nature.com! Connecting neural specialization, population geometry, and their functional implications across the cortical hierarchy. So grateful for this beautiful and fun collaboration with @shuqiw.bsky.social, S Muscinelli, L Paninski, and @stefanofusi.bsky.social!
nature.com
Rarely categorical, highly separable representations along the cortical hierarchy - Nature
Cortical circuits prioritize diversity over categorical structure, supporting a computational regime geared towards high-dimensional, highly separable neural representations.
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Jonna Singh @jonnasingh.bsky.social · 09/06/2026
congrats dio! Lookin NICE
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The Transmitter @thetransmitter.bsky.social · 01/06/2026
A hackathon reveals that disagreement in neuroscience runs deeper than most researchers suspect—even in electrophysiology, a field that prides itself on hard data, write @mattiachini.bsky.social and Gaelle Chapuis. #neuroskyence www.thetransmitter.org/reproducibil...
thetransmitter.org
18 teams analyzed a neuro dataset and got different answers
Disagreement in neuroscience runs deeper than most researchers suspect—even in electrophysiology, a field that prides itself on hard data.
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Jenna Norton @jenna-m-norton.bsky.social · 30/05/2026
Stopping Vought’s proposed rule will be critical to save science and future cures. @standupforscience.net created an action center to help you comment and contact Congress. Time to get loud! fight2win.standupforscience.net
fight2win.standupforscience.net
Stand up for Science
Stand up for Science
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 30/05/2026
If you are going to comment on the proposed changes to how science is done in the US, please use this guide. The rules specify that you have to mention the number associated with the proposed changes, and this blog has those. Here is where to comment: www.federalregister.gov/documents/20...
federalregister.gov
Regulation for Federal Financial Assistance
The Office of Management and Budget (OMB) proposes to revise the Guidance for Federal Financial Assistance to improve government- wide policies and requirements related to the management of grants, co...
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Jeremy Berg @jeremymberg.bsky.social · 30/05/2026
Ways to push back against the proposed OMB regulations fight2win.standupforscience.net
Front page from Stand Up for Science site regarding the proposed OMB regulations
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Jonna Singh @jonnasingh.bsky.social · 30/05/2026
I often feel like “a neural circuit for X” papers might as well be Ireland bricks
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Jonna Singh @jonnasingh.bsky.social · 29/05/2026
umm uncalled for bird hate???? more like musical colorful magnet minigods
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Jonna Singh @jonnasingh.bsky.social · 24/05/2026
so interesting and thoughtful as always - any chance there's a recording of any talk you've given on this? i find those useful for getting a bit more intuition
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Carsen Stringer @computingnature.bsky.social · 22/05/2026
🚨🧠 Our paper is out! We introduce a simple computational model that generates macroscopic, long-timescale dynamics as seen in large-scale neural recordings. #neuroscience #dynamics @marius10p.bsky.social @zhong-lin.bsky.social @hhmijanelia.bsky.social Link: go.nature.com/4tRNjIu
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Ian Oldenburg @ianoldenburg.bsky.social · 19/05/2026
We are hiring a postdoc! We study neural activity and movement using holographic optogenetics, imaging, and recordings in awake mice. My first postdoc, Masashi, is starting his own lab, so now we have an opening. Seeking candidates excited about circuits, optics, coding, or ephys. oldenburglab.com
oldenburglab.com
Oldenburg Lab
Decoding the motor system through the use of multiphoton holographic optogenetics.
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Dr Kathleen Millen @neurodevkathy.bsky.social · 20/05/2026
🚨🧪🧵URGENT INPUT NEEDED: NIH asks input for next strategic plan-including emphasis on non-animal models (NAMs) to replace animals. Per NIH insider, anti-animal responses now outnumber scientists 200-700x. Please please provide input. Deadline: May 26, 11:59 PM ET. grants.nih.gov/news-events/...
grants.nih.gov
NIH Seeks Input on Framework for Next NIH-Wide Strategic Plan | Grants & Funding
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Sarah McAnulty, Ph.D. @sarahmackattack.bsky.social · 18/05/2026
I need your help. When I'm making projects happen, I don't have as much time to remind people to buy merch/donate to Skype a Scientist. SO our balance sheet is...oh dear 😅 If you're able, becoming a monthly donor, even a couple bucks a month, would be really amazing. givebutter.com/SupportSAS26
givebutter.com
Support Skype a Scientist!
By Skype a Scientist
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Paul Kristian LaFosse @lafosse.bsky.social · 15/05/2026
🚨 Ever wanted a simple way to control the activity of thousands of neurons? We introduce an all-optical raster photostimulation method to do just that! w/ @computingnature.bsky.social @marius10p.bsky.social #FluorescenceFriday #neuroskyence www.biorxiv.org/content/10.6... 1/n
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Jonna Singh @jonnasingh.bsky.social · 13/05/2026
Baby steps, this is a way cooler application though i gotta say — go Sam too!
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Jonna Singh @jonnasingh.bsky.social · 13/05/2026
Really cool, and also very satisfying to see a systematic test of the role of these synapses whose role has been heavily assumed and never experimentally tackled! Congrats and to @jmxpearson.bsky.social too!
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Madelyn Hjort @mmhjort.bsky.social · 06/05/2026
Thrilled to share our work out in @nature.com today! Linking flexibility modeling, single-cell imaging, and targeted optogenetics allowed us to characterize how some prefrontal neurons, and mPFC-VTA neurons in particular, drive contingency degradation behavior. www.nature.com/articles/s41...
nature.com
Prefrontal to ventral tegmental area dynamics drive contingency degradation - Nature
This work provides a mechanistic understanding of how certain prefrontal circuits in the rodent brain permit flexibility to selectively stop learned behaviours through interactions with core subcortic...
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Jonna Singh @jonnasingh.bsky.social · 30/04/2026
I love this idea so much
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Jeremiah Cohen @jeremiahycohen.bsky.social · 13/04/2026
Delighted to share our discoveries about one of the brain's neurotransmitter systems: www.biorxiv.org/content/10.6... Together with colleagues at the @alleninstitute.org, we have learned a lot about a tiny cluster of neurons in the brainstem locus coeruleus (LC) that releases norepinephrine (NE). 1
biorxiv.org
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Jonna Singh @jonnasingh.bsky.social · 11/03/2026
Eager to learn how one shanks a P10 rat with a neuropixels Very cool stuff
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Jonna Singh @jonnasingh.bsky.social · 09/03/2026
(sorry)
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Jonna Singh @jonnasingh.bsky.social · 09/03/2026
alpenglow!
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Jonna Singh @jonnasingh.bsky.social · 06/03/2026
1) Why is this the first I’m learning about fish talking to each other by slapping their bellies 2) The actual results in this paper are awesome
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Jonna Singh @jonnasingh.bsky.social · 03/03/2026
how a small (~15) prolific and opinionated set of reviewers could steer a field over time This is great, and even these numbers underestimate the effect. Some fields have <10 qualified reviewers, one loud voice can tank or lift papers on its own
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Jason Moore @moorejh.bsky.social · 24/02/2026
Our perspectives piece on Agentic AI for biomedical research has been published in Nature Biotechnology www.nature.com/articles/s41... #agenticAI #artificialintelligence #agents
nature.com
Agentic AI and the rise of in silico team science in biomedical research - Nature Biotechnology
This study examines the emerging use of agentic artificial intelligence (AI) in biomedical research, highlighting the challenges and opportunities that may inform the design of agentic AI systems suit...
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Pat Savage @patrickesavage.bsky.social · 23/02/2026
Science has now published our eLetter responding to Rajendran et al., titled, “Data show that macaques do not synchronize to a beat” doi.org/10.1126/scie...
doi.org
Monkeys have rhythm
Synchronizing movements to music is a hallmark of human culture, but its evolutionary and neurobiological origins remain unknown. This ability requires (i) extracting a steady rhythmic pulse, or beat,...
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Jonna Singh @jonnasingh.bsky.social · 18/02/2026
For all the energy we use in developing new technologies and fancier data handling, this is an immediate, actionable problem that we need to prioritize Beautifully written!
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Yoav Livneh @yoavlivneh.bsky.social · 13/02/2026
New lab preprint! Can we study conscious perception of gut sensations in mice to reveal its neuronal basis? Can we train mice to report their gut sensations? Omer Rafael and Stav Shtiglitz in the lab teamed up to discover that…YES! Thread…1/6 www.biorxiv.org/content/10.6...
biorxiv.org
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Jonna Singh @jonnasingh.bsky.social · 12/02/2026
Almost feels wrong to see suite2p as a paper after all these years, used to it being a more of a silent pillar
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adamezracohen.bsky.social @adamezracohen.bsky.social · 04/01/2026
What is the computational role of dendritic excitations? Byung Hun Lee and team mapped voltage dynamics throughout the dendritic trees of CA1 pyramidal neurons in mice navigating in virtual reality. www.biorxiv.org/content/10.6...
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Yoav Livneh @yoavlivneh.bsky.social · 12/12/2025
lab preprint! Interopceptive predictions are central to many brain-body interactions theories, but it's unclear if/how they affect bodily physiology. We (fearless Einav Litvak et al) show that insular cortex predictions are essential for glucose homeostasis-THREAD.. www.biorxiv.org/content/10.6...
biorxiv.org
Insular cortex predictions regulate glucose homeostasis
Brain-body interactions are essential for physical and emotional homeostasis. The brain uses information from the external world to predict upcoming bodily changes. This process involves interoceptive...
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Alex Kwan @alexkwan.bsky.social · 05/12/2025
We used rabies virus 👾 to map how #psilocybin modifies long-range circuits 🧠, revealing network-specific reorganization that we didn’t expect. The full study is now online at Cell. @cp-cell.bsky.social Paper 👉 www.cell.com/cell/fulltex... Thread for a synopsis 👉 bsky.app/profile/alex...
cell.com
Psilocybin triggers an activity-dependent rewiring of large-scale cortical networks
Psilocybin reshapes brain networks through activity-dependent plasticity, including a weakening of recurrent cortical loops that could underlie its therapeutic effects.
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The Transmitter @thetransmitter.bsky.social · 24/11/2025
In @thetransmitter.bsky.social’s Rising Stars of Neuroscience 2025, we recognize 25 early-career researchers who have made outstanding scientific contributions and demonstrated a commitment to mentoring and community-building in neuroscience. #neuroskyence #StateOfNeuroscience bit.ly/4rnFnyQ
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Jonna Singh @jonnasingh.bsky.social · 18/11/2025
Gracias Carlos!! Nos vemos en opto GRC o neuromodulation GRC estos años?
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Jonna Singh @jonnasingh.bsky.social · 18/11/2025
thank you Anne, I miss Duke but at least i still have like 10 neurobio Dukies here (:
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Jonna Singh @jonnasingh.bsky.social · 17/11/2025
great to hear from you Cam! come visit us
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