Peter Rupprecht
@ptrrupprecht.bsky.social
Junior group leader in neuroscience - calcium imaging, ephys, plasticity, microscopy, neurons & astrocytes, data analysis. PhD with Rainer Friedrich, postdoc with Fritjof Helmchen. https://www.gcamp6f.com/
Pinned
Peter Rupprecht
@ptrrupprecht.bsky.social
· Mar 11
Are you using GCaMP8 or are planning to switch from GCaMP6? Then check out this new preprint from our lab! www.biorxiv.org/content/10.1...
- Calcium imaging
- GCaMP8 vs. GCaMP6
- Spike inference
- Imaging + ephys ground truth
With F. Helmchen, K. Svoboda, M. Rozsa & X. Fang.
- Calcium imaging
- GCaMP8 vs. GCaMP6
- Spike inference
- Imaging + ephys ground truth
With F. Helmchen, K. Svoboda, M. Rozsa & X. Fang.
Reposted by Peter Rupprecht
Independent NeuroScience Services INSS was registered as a company on 14th November 2016, which means it's our 9th birthday today! As a birthday present we've treated ourselves to an SfN exhibitor booth for the first time ever. Come and say hello at Booth #3327
November 15, 2025 at 12:03 AM
Independent NeuroScience Services INSS was registered as a company on 14th November 2016, which means it's our 9th birthday today! As a birthday present we've treated ourselves to an SfN exhibitor booth for the first time ever. Come and say hello at Booth #3327
New blog post, where I highlight a few interesting papers on astrocyte ultrastructure and function, with papers from the labs of Moritz Helmstädter @mhlab.bsky.social, Kristen Harris, Andrea Volterra, Karin Pernet-Gallay, and Hailan Hu: gcamp6f.com/2025/11/14/i...
Interesting papers on astrocyte ultrastructure and function
Astrocytes are brain cells that are often completely overlooked and dismissed or, in the opposite extreme, presented as mysterious devices that somehow solve all problems of computational neuroscie…
gcamp6f.com
November 14, 2025 at 12:27 PM
New blog post, where I highlight a few interesting papers on astrocyte ultrastructure and function, with papers from the labs of Moritz Helmstädter @mhlab.bsky.social, Kristen Harris, Andrea Volterra, Karin Pernet-Gallay, and Hailan Hu: gcamp6f.com/2025/11/14/i...
Reposted by Peter Rupprecht
How did I not know about this super-useful site for customized 3D-printable thread adapters? HT to @leon-kremers.bsky.social : brainright.com/adapt-o-matic/
Jay’s Adapt~O~Matic – BrainRight
brainright.com
November 5, 2025 at 11:02 AM
How did I not know about this super-useful site for customized 3D-printable thread adapters? HT to @leon-kremers.bsky.social : brainright.com/adapt-o-matic/
Reposted by Peter Rupprecht
The long wait is finally over: The @thorlabs.bsky.social 8 kHz resonant scanner is available 🔬! It would be lovely if there would be a 30 mm cube compatible & acoustically shielded mount as well, but I'm sure that's going to come eventually! #Microscopy www.thorlabs.com/newgrouppage...
October 22, 2025 at 6:47 PM
The long wait is finally over: The @thorlabs.bsky.social 8 kHz resonant scanner is available 🔬! It would be lovely if there would be a 30 mm cube compatible & acoustically shielded mount as well, but I'm sure that's going to come eventually! #Microscopy www.thorlabs.com/newgrouppage...
Reposted by Peter Rupprecht
Understanding behavior requires datasets that capture humans while carrying out complex tasks. The kitchen is an excellent environment for assessing human motor and cognitive function, as many complex actions are naturally exhibited in kitchens from chopping to 🧽!
arxiv.org/abs/2506.01608
arxiv.org/abs/2506.01608
EPFL-Smart-Kitchen-30: Densely annotated cooking dataset with 3D kinematics to challenge video and language models
Understanding behavior requires datasets that capture humans while carrying out complex tasks. The kitchen is an excellent environment for assessing human motor and cognitive function, as many complex...
arxiv.org
September 23, 2025 at 7:18 AM
Understanding behavior requires datasets that capture humans while carrying out complex tasks. The kitchen is an excellent environment for assessing human motor and cognitive function, as many complex actions are naturally exhibited in kitchens from chopping to 🧽!
arxiv.org/abs/2506.01608
arxiv.org/abs/2506.01608
Reposted by Peter Rupprecht
« Diverse calcium dynamics underlie place field formation in hippocampal CA1 pyramidal cells. »
A fundamental study now published @elife.bsky.social
elifesciences.org/reviewed-pre...
A fundamental study now published @elife.bsky.social
elifesciences.org/reviewed-pre...
September 17, 2025 at 12:05 PM
« Diverse calcium dynamics underlie place field formation in hippocampal CA1 pyramidal cells. »
A fundamental study now published @elife.bsky.social
elifesciences.org/reviewed-pre...
A fundamental study now published @elife.bsky.social
elifesciences.org/reviewed-pre...
New blog post about a fun project where I tried to beautify my office by putting a poster of the hippocampal column onto my walls: gcamp6f.com/2025/08/13/d...
EM pictures from this paper: www.biorxiv.org/content/10.1... from the lab of @helenelab.bsky.social
EM pictures from this paper: www.biorxiv.org/content/10.1... from the lab of @helenelab.bsky.social
Displaying the hippocampus as EM image on the office wall
One of the most amazing methods in modern neuroscience is dense volumetric electron microscopy of the brain. I have mentioned some openly accessible datasets before (see my previous blog post), but…
gcamp6f.com
August 14, 2025 at 8:27 AM
New blog post about a fun project where I tried to beautify my office by putting a poster of the hippocampal column onto my walls: gcamp6f.com/2025/08/13/d...
EM pictures from this paper: www.biorxiv.org/content/10.1... from the lab of @helenelab.bsky.social
EM pictures from this paper: www.biorxiv.org/content/10.1... from the lab of @helenelab.bsky.social
New blog post, where I review some recent interesting papers on the role of cell organelles for neuronal calcium signaling: gcamp6f.com/2025/08/11/i...
Featuring work by @lorenabenedetti.bsky.social, O'Hare et al. and Lin et al.!
Featuring work by @lorenabenedetti.bsky.social, O'Hare et al. and Lin et al.!
Interesting papers on the role of cell organelles in neuronal dendrites for calcium signaling
Researchers utilize calcium imaging to track neuronal activity in the brain, highlighting the role of calcium as a signaling molecule. Recent studies investigate intracellular calcium dynamics, par…
gcamp6f.com
August 11, 2025 at 12:19 PM
New blog post, where I review some recent interesting papers on the role of cell organelles for neuronal calcium signaling: gcamp6f.com/2025/08/11/i...
Featuring work by @lorenabenedetti.bsky.social, O'Hare et al. and Lin et al.!
Featuring work by @lorenabenedetti.bsky.social, O'Hare et al. and Lin et al.!
Reposted by Peter Rupprecht
#OCaMP is now on bioRxiv and reagents are available on #Addgene! 🧪
A sensitive orange fluorescent calcium ion indicator for imaging neural activity
www.biorxiv.org/content/10.1...
A sensitive orange fluorescent calcium ion indicator for imaging neural activity
www.biorxiv.org/content/10.1...
A sensitive orange fluorescent calcium ion indicator for imaging neural activity
Genetically encoded calcium indicators (GECIs) are vital tools for fluorescence-based visualization of neuronal activity with high spatial and temporal resolution. However, current highest-performance...
www.biorxiv.org
July 31, 2025 at 7:34 PM
#OCaMP is now on bioRxiv and reagents are available on #Addgene! 🧪
A sensitive orange fluorescent calcium ion indicator for imaging neural activity
www.biorxiv.org/content/10.1...
A sensitive orange fluorescent calcium ion indicator for imaging neural activity
www.biorxiv.org/content/10.1...
New blog post with a review of interesting papers on VIP interneurons in cortex and hippocampus: gcamp6f.com/2025/06/23/i...
Covering work from @koenvervaeke.bsky.social's lab with @mateneubrandt.bsky.social, Yoav Adam's lab and Bernardo Rudy's lab.
Covering work from @koenvervaeke.bsky.social's lab with @mateneubrandt.bsky.social, Yoav Adam's lab and Bernardo Rudy's lab.
June 23, 2025 at 1:04 PM
New blog post with a review of interesting papers on VIP interneurons in cortex and hippocampus: gcamp6f.com/2025/06/23/i...
Covering work from @koenvervaeke.bsky.social's lab with @mateneubrandt.bsky.social, Yoav Adam's lab and Bernardo Rudy's lab.
Covering work from @koenvervaeke.bsky.social's lab with @mateneubrandt.bsky.social, Yoav Adam's lab and Bernardo Rudy's lab.
Reposted by Peter Rupprecht
#neuroskyence folks: as my postdoc grant is running out soon, I am looking for new opportunities in systems neuroscience!
Keywords: patch clamp ephys, opto, mouse behavior, (in vivo) voltage imaging. Would love to return to the Basal Ganglia.
Sharing appreciated, and happy #FluorescenceFriday !
Keywords: patch clamp ephys, opto, mouse behavior, (in vivo) voltage imaging. Would love to return to the Basal Ganglia.
Sharing appreciated, and happy #FluorescenceFriday !
June 13, 2025 at 1:33 PM
#neuroskyence folks: as my postdoc grant is running out soon, I am looking for new opportunities in systems neuroscience!
Keywords: patch clamp ephys, opto, mouse behavior, (in vivo) voltage imaging. Would love to return to the Basal Ganglia.
Sharing appreciated, and happy #FluorescenceFriday !
Keywords: patch clamp ephys, opto, mouse behavior, (in vivo) voltage imaging. Would love to return to the Basal Ganglia.
Sharing appreciated, and happy #FluorescenceFriday !
Reposted by Peter Rupprecht
It is out! Read how you achieve 1.7 mm deep 3-photon imaging in prefrontal cortex with dendritic spine resolution over a week.
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Three-photon in vivo imaging of neurons and glia in the medial prefrontal cortex with sub-cellular resolution - Communications Biology
Three-photon in vivo imaging provides access to medial prefrontal cortex, hippocampus and spinal cord in mice at up to 1.7 mm depth of neurons, dendrites, spines, astrocytes and microglia.
www.nature.com
June 1, 2025 at 9:58 AM
It is out! Read how you achieve 1.7 mm deep 3-photon imaging in prefrontal cortex with dendritic spine resolution over a week.
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted by Peter Rupprecht
1/6 Why does the brain maintain such precise excitatory-inhibitory balance?
Our new preprint explores a provocative idea: Small, targeted deviations from this balance may serve a purpose: to encode local error signals for learning.
www.biorxiv.org/content/10.1...
led by @jrbch.bsky.social
Our new preprint explores a provocative idea: Small, targeted deviations from this balance may serve a purpose: to encode local error signals for learning.
www.biorxiv.org/content/10.1...
led by @jrbch.bsky.social
May 27, 2025 at 7:49 AM
1/6 Why does the brain maintain such precise excitatory-inhibitory balance?
Our new preprint explores a provocative idea: Small, targeted deviations from this balance may serve a purpose: to encode local error signals for learning.
www.biorxiv.org/content/10.1...
led by @jrbch.bsky.social
Our new preprint explores a provocative idea: Small, targeted deviations from this balance may serve a purpose: to encode local error signals for learning.
www.biorxiv.org/content/10.1...
led by @jrbch.bsky.social
Reposted by Peter Rupprecht
The culmination of years of hard work by Anna Maria Reuss & Co: aDISCO - a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue! With lots of @mesospim.bsky.social #lightsheet #Microscopy @ptrrupprecht.bsky.social & many more!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
May 27, 2025 at 7:30 AM
The culmination of years of hard work by Anna Maria Reuss & Co: aDISCO - a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue! With lots of @mesospim.bsky.social #lightsheet #Microscopy @ptrrupprecht.bsky.social & many more!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Peter Rupprecht
Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching.
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
May 12, 2025 at 5:25 AM
Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching.
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...
Our study on spike inference from calcium imaging data in spinal cord is now published at the Journal of Neuroscience @sfnjournals.bsky.social ! 🥳With open datasets and public reviews: www.jneurosci.org/content/45/1...
Spike Rate Inference from Mouse Spinal Cord Calcium Imaging Data
Calcium imaging is a key method to record the spiking activity of identified and genetically targeted neurons. However, the observed calcium signals are only an indirect readout of the underlying elec...
www.jneurosci.org
May 6, 2025 at 4:44 PM
Our study on spike inference from calcium imaging data in spinal cord is now published at the Journal of Neuroscience @sfnjournals.bsky.social ! 🥳With open datasets and public reviews: www.jneurosci.org/content/45/1...
Reposted by Peter Rupprecht
Super happy that our papers #2 and #3 from our 3-person lab just went online on bioRxiv! First large-scale 3D EM dataset from mouse hippocampus CA1 www.biorxiv.org/content/10.1... - check out the beautiful data on webknossos wklink.org/7023 ! …
April 23, 2025 at 7:20 AM
Super happy that our papers #2 and #3 from our 3-person lab just went online on bioRxiv! First large-scale 3D EM dataset from mouse hippocampus CA1 www.biorxiv.org/content/10.1... - check out the beautiful data on webknossos wklink.org/7023 ! …
The BlueSpot Talk is a seminar series about the locus coeruleus organized by David Weinshenker.
Today at 11 AM EST or 5 PM CET, I'll give a talk: "Effects of locus coeruleus on hippocampal astrocytes and neurons during natural and artificial arousal"
zoom.us/j/99332227402
Today at 11 AM EST or 5 PM CET, I'll give a talk: "Effects of locus coeruleus on hippocampal astrocytes and neurons during natural and artificial arousal"
zoom.us/j/99332227402
April 21, 2025 at 11:22 AM
The BlueSpot Talk is a seminar series about the locus coeruleus organized by David Weinshenker.
Today at 11 AM EST or 5 PM CET, I'll give a talk: "Effects of locus coeruleus on hippocampal astrocytes and neurons during natural and artificial arousal"
zoom.us/j/99332227402
Today at 11 AM EST or 5 PM CET, I'll give a talk: "Effects of locus coeruleus on hippocampal astrocytes and neurons during natural and artificial arousal"
zoom.us/j/99332227402
New blog post on online spike inference from calcium imaging data with deep learning: gcamp6f.com/2025/03/24/o...
Online spike inference with GCaMP8
Calcium imaging is used to record the activity of neurons in living animals. Often, these activity patterns are analyzed after the experiments to investigate how the brain works. Alternatively, it …
gcamp6f.com
March 24, 2025 at 3:16 PM
New blog post on online spike inference from calcium imaging data with deep learning: gcamp6f.com/2025/03/24/o...
Reposted by Peter Rupprecht
That was a fun project! Thanks to Rob Lees, Adam Packer, and all the co-authors for inviting me to participate.
rdcu.be/edQXi
rdcu.be/edQXi
Standardized measurements for monitoring and comparing multiphoton microscope systems
Nature Protocols - A set of procedures is described here for standardizing the evaluation of multiphoton microscope performance, covering laser power, pulse width optimizations, field of view,...
rdcu.be
March 17, 2025 at 12:08 PM
That was a fun project! Thanks to Rob Lees, Adam Packer, and all the co-authors for inviting me to participate.
rdcu.be/edQXi
rdcu.be/edQXi
Reposted by Peter Rupprecht
Question for my neurobiology colleagues: what (if any) information do second messengers in neurons carry about their specific synapse of origin? In other words, if I were to measure only molecular signals in the soma, to what extent could I resolve a specific pattern of synaptic activation?
March 16, 2025 at 5:11 PM
Question for my neurobiology colleagues: what (if any) information do second messengers in neurons carry about their specific synapse of origin? In other words, if I were to measure only molecular signals in the soma, to what extent could I resolve a specific pattern of synaptic activation?
New blog post: Non-linearity of calcium indicators: history-dependence of spike reporting gcamp6f.com/2025/03/14/n..., highlighting an interesting analysis of our recent preprint.
March 14, 2025 at 12:07 PM
New blog post: Non-linearity of calcium indicators: history-dependence of spike reporting gcamp6f.com/2025/03/14/n..., highlighting an interesting analysis of our recent preprint.
Technically very interesting new paper from Na Ji's lab using an upgrade of their FACED technology for ultrafast (~1000 fps) two-photon scanning for voltage and calcium imaging: www.biorxiv.org/content/10.1...
FACED 2.0 enables large-scale voltage and calcium imaging in vivo
Monitoring neuronal activity at large scale and high spatiotemporal resolution is crucial for understanding information processing within the brain. We optimized a kilohertz-frame-rate two-photon fluo...
www.biorxiv.org
March 14, 2025 at 11:10 AM
Technically very interesting new paper from Na Ji's lab using an upgrade of their FACED technology for ultrafast (~1000 fps) two-photon scanning for voltage and calcium imaging: www.biorxiv.org/content/10.1...
Are you using GCaMP8 or are planning to switch from GCaMP6? Then check out this new preprint from our lab! www.biorxiv.org/content/10.1...
- Calcium imaging
- GCaMP8 vs. GCaMP6
- Spike inference
- Imaging + ephys ground truth
With F. Helmchen, K. Svoboda, M. Rozsa & X. Fang.
- Calcium imaging
- GCaMP8 vs. GCaMP6
- Spike inference
- Imaging + ephys ground truth
With F. Helmchen, K. Svoboda, M. Rozsa & X. Fang.
March 11, 2025 at 11:30 AM
Are you using GCaMP8 or are planning to switch from GCaMP6? Then check out this new preprint from our lab! www.biorxiv.org/content/10.1...
- Calcium imaging
- GCaMP8 vs. GCaMP6
- Spike inference
- Imaging + ephys ground truth
With F. Helmchen, K. Svoboda, M. Rozsa & X. Fang.
- Calcium imaging
- GCaMP8 vs. GCaMP6
- Spike inference
- Imaging + ephys ground truth
With F. Helmchen, K. Svoboda, M. Rozsa & X. Fang.
Reposted by Peter Rupprecht
How much analgesia is needed to manage pain levels in mice after brain surgeries?
A single dose of meloxicam seems to be enough. Even the addition of opioids cannot provide a clear benefit. (in line with recent work from others, see cites in our preprint): www.biorxiv.org/content/10.1...
A single dose of meloxicam seems to be enough. Even the addition of opioids cannot provide a clear benefit. (in line with recent work from others, see cites in our preprint): www.biorxiv.org/content/10.1...
GrimACE: Automated, multimodal cage-side assessment of pain and well-being in mice
Pain and welfare monitoring is essential for ethical animal testing, but current cage-side assessments are qualitative and subjective. Here we present the GrimACE, the first fully standardised and aut...
www.biorxiv.org
March 11, 2025 at 7:00 AM
How much analgesia is needed to manage pain levels in mice after brain surgeries?
A single dose of meloxicam seems to be enough. Even the addition of opioids cannot provide a clear benefit. (in line with recent work from others, see cites in our preprint): www.biorxiv.org/content/10.1...
A single dose of meloxicam seems to be enough. Even the addition of opioids cannot provide a clear benefit. (in line with recent work from others, see cites in our preprint): www.biorxiv.org/content/10.1...