Peter Rupprecht

Very excited about this preprint! We present a new method to flexibly align your 2P imaging plane with curved biological structures. Great work of PhD student Shinjini Ghosh, with Fritjof Helmchen, @nvladimus.bsky.social, and many others! www.biorxiv.org/content/10.6...

[1/3] It was a lot of fun to work on optical simulations for real-world use cases of a K-mirror (image rotator) in two-photon microscopes with Shinjini Gosh, @ptrrupprecht.bsky.social, and the team. There are a few things that I learned on the way.

We posted a preprint on all-to-all functional mapping of a cortical microcircuit in vivo. biorxiv.org/content/10.6... Yitong Qi developed molecular tools, optics, and protocols for massively parallel optogenetic stimulation and voltage imaging during animal behavior.

Preprint is out! Our BakingTray software turns a 2-photon microscope into a serial-section tomography system for automated whole-organ imaging. ~€35k to convert an existing scope. 11 systems worldwide, >7,000 samples at SWC alone #neuroskyence #microscopy www.biorxiv.org/content/10.6...

Precise structural and functional organization of the olfactory bulb neuropil early in development, revealed by volume EM, dense reconstruction and 2P calcium imaging in zebrafish. Great work by Ruth and others in collaboration with @michalwj.bsky.social www.biorxiv.org/content/10.6...

Just out in Nat Neurosci: disentangling of neural odor manifolds in "olfactory cortex" of adult zebrafish after learning. Great work by Bo, Nesibe et al and wonderful collaboration with @sueyeonchung.bsky.social that fundamentally changed my view of olfactory cortex. www.nature.com/articles/s41...

🚨 Now out in @aaas.org Science Advances 🚨: aDISCO: a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue by Anna Maria Reuss! 🧠🔬#lightsheet #Microscopy @mesospim.bsky.social @ptrrupprecht.bsky.social www.science.org/doi/10.1126/...

Happy to share the CA3 dataset is published. First large-scale dense connectomics from hippocampus. First connectomic dataset imaged in @princetonneuro.bsky.social. A harbinger of many larger datasets to come (for both). doi.org/10.1038/s415... #hippocampus But my personal favorite is (1/2)

This is very solid work. It prompts a question I have never had a satisfying answer for: why do people want to infer spikes from calcium imaging data? The calcium signal contains sufficient information for *any* inference procedure, and none of the bias. Why don't people work directly with calcium?

Excited to share our work now in Nature Methods! We wrote this manuscript to help others better analyze and interpret calcium imaging data. As a central aspect, we show why nonlinear behavior of calcium indicators matters in practice. Very happy about this work!

An Analysis from @ptrrupprecht.bsky.social et al investigates the behavior of GCaMP8 variants in spike inference using different algorithms. www.nature.com/articles/s41...

@ptrrupprecht.bsky.social providing the new go-to GECI reference. Read when doing calcium imaging. rdcu.be/fwF82

If you miss science twitter, maybe you should join NeuroMethods on zulip (similar to slack but better): neuromethods.zulipchat.com/login/ If you have no idea what this is about, here's a brief blog post with the history: gcamp6f.com/2026/07/21/n...

The @ptrrupprecht.bsky.social lab uses a really cool approach combining neuromodulator imaging, optogenetics, and two-photon calcium imaging to determine how locus coeruleus-mediated norepinephrine signaling influences different hippocampal cell types, including #astrocytes.

@ptrrupprecht.bsky.social can you give an estimate for the difference in baseline brightness between GCaMP8s and 6f?

I wanted to like QED's new 1% preprint ranking. I really did. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review. open.substack.com/pub/blekhman...

The YouTube channel of @kurzgesagt.org made a great and accessible video on how memories are stored in our brains. I wrote a blog post to provide additional context and details for those interested in the view of a neurophysiology researcher: gcamp6f.com/2026/06/22/w...

I honestly hate watching talks made with AI. I hate it when speakers brag about how much time it saved them. If you have 80 people in your audience and they all watch you for 30 minutes, that's 40 hours of person-time. And you're telling us you're *proud* of how little you prepared? 🤷‍♀️

Two brain circuits. Same learning problem. Shared learning outcomes. Different dynamical implementations. Our work shows that learning is not a single canonical solution but can emerge through distinct population dynamics shaped by circuit architecture. Excited to share our latest preprint! 🧵1/12

We're thrilled to share this #Perspective @natneuro.nature.com on #astrocytes as a multilayered system of #functional #units that operate across spatial scales. 👉Available for reading here: rdcu.be/fk0B7 👉Full article here: www.nature.com/articles/s41...

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

Finally online @natmethods.nature.com www.nature.com/articles/s41... This was a fun collaboration with @finkryan.bsky.social @massecklab.bsky.social @tpatriarchi.bsky.social @martinfuhrmann.bsky.social @campbell-lab.bsky.social @jangrundemann.bsky.social 🧪🧠🔬🧬

🧪 1/ New preprint from the lab: L5 pyramidal cell tLTD requires astrocyte Ca2+ and CB1 signaling www.biorxiv.org/content/10.6... We revisit a classic STDP result in visual cortex

1/8. New preprint! Using fUSi in head-fixed mice🐭, we found that arousal events trigger a brain-wide wave of activity 🌊🧠. Surprisingly, this pattern was preserved during opto manipulations of the locus coeruleus, pointing to a minor role for noradrenergic tone. www.biorxiv.org/content/10.6...

First whole-brain recording of social sound processing in a vertebrate. Surprises start in the hindbrain; thalamus gates conspecific calls; male and female brains diverge downstream. Work by @joerghenninger.bsky.social, @mh123.bsky.social sky.social and team. www.biorxiv.org/content/10.6...

Two-photon calcium imaging at 24,000 lines/s, with the resonant axis spanning 4x what other systems can do. Inertia-free. Diffraction-limited. No tradeoffs. Che-Hang Yu developed a 4x angle multiplier for laser scanning. His paper is out today: opg.optica.org/optica/fullt... 1/n #fluorescenceFriday

First time patching in months, y'all know what that means: I am about to spend the next few hours discovering fun and novel ways in which an ephys setup can break!

A new preprint introduces aDISCO, a DISCO-based clearing approach that makes whole archival FFPE human tissues transparent and antibody-compatible, enabling true 3D light-sheet histology across brain & multiple organs at cellular resolution. Aguzzi & Helmchen teams. www.biorxiv.org/content/10.1...

But then where do the branch-specific variations in voltage come from? We found that in apical dendrites, small subthreshold depolarizations *preceding* a complex spike partially predict voltage (and Ca2+) amplitude *during* the event. This suggests conjunctive amplification of inputs and spikes.

What's the relation between voltage and calcium in dendrites? Xiang Wu studied this in CA2 hippocampal pyramidal cells in behaving mice. www.biorxiv.org/content/10.6...