Assistant prof at Baylor College of Medicine. Sensory circuits & brain state modulation. Imaging, patching, and pupils. Kiddo dad. Opinions are my own. (he/him)

Houston, TX
Joined June 2009
When you say “Just make it work”…
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Jacob Reimer retweeted
#MayThe4th be with you! Meet FORCE1s, a new positive‑going, ultrasensitive voltage indicator. Optimized for 2P imaging at slower acquisition speeds, FORCE1s is easy to use on almost any microscope. Bonus: it even powers 2P miniscope experiments!📄Preprint: biorxiv.org/content/10.64898…
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Jacob Reimer retweeted
#MayThe4th announcement: JEDI-2P was not The Last Jedi ⚔️! Introducing JEDI3sub & JEDI3hyp, the best GEVIs in this galaxy for reporting subthresholds voltage dynamics under two-photon illumination🔬#GEVIs. Check out our @naturemethods paper: nature.com/articles/s41592-0…
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Jacob Reimer retweeted
Every experimental neuroscientist knows the feeling: you have a hypothesis, but running the experiment takes months👩‍🔬 In our new preprint @biorxiv_neursci , we present an openly available functional ''digital twin'' of the retinal input to the mouse superior colliculus that lets you test hypotheses in the model first — try it out yourself using the link below 🧠 We combined chronic two-photon imaging of >200k retinal ganglion cell axonal boutons in the mouse superior colliculus (SC) with deep dynamic models that predict neural responses to parametric light stimuli and natural movies. Key findings⚡️ ▸ Retinal inputs to the SC form functionally distinct, laminar-organized response types, identified via Gaussian mixture model clustering ▸ The functional diversity of retinal output matches that of retinal input to the SC. We show this by aligning our dataset with a retinal reference dataset using a variational autoencoder with adversarial training ▸ Our deep dynamic digital twin learns stimulus–response transformations and generalizes to stimuli it was never trained on, including parametric stimuli used for cell type identification The model functions as a virtual lab bench: feed in any stimulus you're curious about and generate predicted neural responses. As a proof of concept, we fed in a looming stimulus — known to trigger defensive behavior in mice — and identified putative response types selective for this stimulus Try it in our Colab notebook with your own stimulus and see what the model predicts 📄 Preprint: biorxiv.org/content/10.64898…💻 Colab: colab.research.google.com/dr…📂 Code: github.com/yongrong-qiu/reti… Huge thanks to an incredible cross-institutional team spanning @StanfordMed , @uktuebingen , @uniGoettingen , @bcm_neurosci & many more @YongrongQ, @lisa_schmors, Na Zhou, Mels Akhmetali, Dominic Gonschorek, Cameron Smith, Anton Sumser, Marie Vallens, @crcadwell, Fabrizio Gabbiani, Maximilian Joesch, @AToliasLab, Philipp Berens, Thomas Euler, @sinzlab, @viajake 🙌
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Jacob Reimer retweeted
Chris Xu talks to Neurophotonics about the 'toy land of optics' and how to channel positive vibes! Thank you @TianYuWang2020 for conducting this fantastic interview! spiedigitallibrary.org/journ… #Neurophotonics #Neuroscience #Neuroimaging #BrainImaging #OpticalImaging #Microscopy
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We will likely be looking for someone with expertise with optical methods in vivo, cranial window surgeries in mice, analysis of 2P imaging data (especially ML-based), viral approaches. Nothing posted yet, but I know there are good people looking, so please reach out.
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After 7 years, thrilled to finally share our #MICrONS functional connectomics results! We recorded activity from ~75K neurons in visual cortex in a single mouse, then mapped its wiring using electron microscopy. To systematically characterize neuron function, we built the first foundation model of the mouse visual cortex—trained via deep learning on data pooled from multiple mice and visual cortical areas. Our foundation model generalized to new neurons, animals, and even unseen stimulus domains. It also accurately predicted entirely new modalities, such as anatomically defined cell types. Importantly, this robust generalization enabled us to create accurate functional digital twins of individual mouse brains. Using the digital twin of the MICrONS mouse—where we knew the exact neuronal wiring—we discovered that neurons don’t connect randomly, even when anatomically positioned to do so. Instead, given multiple potential partners (axons near dendrites), neurons preferentially choose partners with similar feature selectivity (“what”) rather than receptive field overlap (“where”). Foundation models offer a powerful approach to systematically decode the neural code of intelligence. Huge thanks to @IARPAnews for funding this groundbreaking effort through the @BRAINinitiative, and to our amazing team at @Stanford @StanfordMed @bcmhouston, @Allen, @Princeton, @uniGoettingen and others! #Neuroscience #MICrONS #NeuroAI #Connectomics #FoundationModels #AI nature.com/immersive/d42859-…
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The most exciting thing about the 10 papers in this cortex edition of Nature is that they are just the beginning of discoveries to be made using the microns dataset. Yours could be next microns-explorer.org
Researchers have created the largest and most detailed wiring diagram of a mammalian brain to date, by mapping cells in a cubic millimetre of a mouse’s brain tissue go.nature.com/3G1eihE
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If you want to feel small and insignificant, stare up at the stars. If you want to feel immensely profound, impossibly complex, and just outright improbable, gaze at the stars in this 1mm cube and realize it's ~ a millionth the volume of your own brain. microns-explorer.org/cortica…
Excited and proud to see all the MICrONS papers out in @NaturePortfolio today, including NEURD - a tool developed in our lab to help with automated proofreading and analysis of large EM connectomes. Check out the beautiful landing page @Nature: nature.com/immersive/d42859-…
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Excited and proud to see all the MICrONS papers out in @NaturePortfolio today, including NEURD - a tool developed in our lab to help with automated proofreading and analysis of large EM connectomes. Check out the beautiful landing page @Nature: nature.com/immersive/d42859-…
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I feel very lucky to have played a role in this huge collaborative project. There's not that many neuroscience projects that have the scale of aspirations, collaborative effort, and scientific payoff of a space mission...
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But over the past ten years I've definitely felt that analogy to a space mission many times. So many essential contributions - both large and small - from so many people to get the project to this point. And there is still so much to discover in this data!
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Some commenting about NIH grants don't appreciate how incredibly competitive it is to get these funds A typical study section reviews ~75-100 grants, most of which are outstanding but only ~10 get funded Can't think of any process in the private sector that is as competitive
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Jacob Reimer retweeted
I am humbled by the response to this and I have one ask. Can you share this post so that we can get 75K likes? It is the most impactful thing @sabrevaya and I can do to save our democracy.
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Seeing a launch in person was amazing. But standing next to a dozen young spacex engineers and seeing their reaction to the catch was a real bonus.
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Me, thinking about all the experiments I proposed that don’t require months in the idyllic Swiss countryside.
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If there was a Nobel prize for steaming milk in your SFN hotel room…
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Seems like there’s no reason in principle the tartrazine trick (with a suitable dye) wouldn’t work in the brain for 2P. Is that right?
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