#calciumimaging — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #calciumimaging, aggregated by home.social.
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Nice #Labrigger post on a point that is easy to forget in #2p #CalciumImaging: Image quality is not just about seeing cells, but about photons/s/neuron.
Larger FOVs are tempting, but they usually mean fewer #photons per cell, lower sensitivity to small Delta F/F events, and more trouble w/ #neuropil contamination. In the end, fidelity is a measurement problem, not just an optics problem:
https://labrigger.com/blog/2026/07/25/2p-calcium-imaging-fidelity/
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Nice #Labrigger post on a point that is easy to forget in #2p #CalciumImaging: Image quality is not just about seeing cells, but about photons/s/neuron.
Larger FOVs are tempting, but they usually mean fewer #photons per cell, lower sensitivity to small Delta F/F events, and more trouble w/ #neuropil contamination. In the end, fidelity is a measurement problem, not just an optics problem:
https://labrigger.com/blog/2026/07/25/2p-calcium-imaging-fidelity/
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🧠New paper by Carneiro-Nascimento et al: awake #invivo #2p #CalciumImaging reveals diverse #CalciumDynamics in #meningeal #macrophages during cortical spreading depolarization (CSD), an aberrant #brain #hyperexcitability event linked to #migraine, #stroke, and #traumatic brain injury. #Neuroscience
Intravital calcium imaging of ... -
🧠New paper by Carneiro-Nascimento et al: awake #invivo #2p #CalciumImaging reveals diverse #CalciumDynamics in #meningeal #macrophages during cortical spreading depolarization (CSD), an aberrant #brain #hyperexcitability event linked to #migraine, #stroke, and #traumatic brain injury. #Neuroscience
Intravital calcium imaging of ... -
🧠 New paper by Carneiro-Nascimento et al: awake #invivo #2p #CalciumImaging reveals diverse #CalciumDynamics in #meningeal #macrophages during cortical spreading depolarization (CSD), an aberrant #brain #hyperexcitability event linked to #migraine, #stroke, and #traumatic brain injury.
📝 https://doi.org/10.7554/eLife.109888
#Neuroimmunology #Neuroscience #imaging @eLife https://fediscience.org/@eLife/116605475951455191
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🧠 New paper by Carneiro-Nascimento et al: awake #invivo #2p #CalciumImaging reveals diverse #CalciumDynamics in #meningeal #macrophages during cortical spreading depolarization (CSD), an aberrant #brain #hyperexcitability event linked to #migraine, #stroke, and #traumatic brain injury.
📝 https://doi.org/10.7554/eLife.109888
#Neuroimmunology #Neuroscience #imaging @eLife https://fediscience.org/@eLife/116605475951455191
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🧠 New paper by Phillips et al: #Neuroplex combines #miniscope #CalciumImaging with multiplexed #SpectralImaging through the same #GRINlens, allowing up to 9 projection-defined #NeuronalPopulations to be identified in freely #behaving mice. Instead of measuring activity alone, the approach links #FunctionalDynamics directly to circuit identity within the same animal and behavioral session.
📝 https://doi.org/10.7554/eLife.110277
#Neuroscience #CompNeuro #NeuralCircuits #Imaging @eLife https://fediscience.org/@eLife/116589668668928682
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🧠 New paper by Phillips et al: #Neuroplex combines #miniscope #CalciumImaging with multiplexed #SpectralImaging through the same #GRINlens, allowing up to 9 projection-defined #NeuronalPopulations to be identified in freely #behaving mice. Instead of measuring activity alone, the approach links #FunctionalDynamics directly to circuit identity within the same animal and behavioral session.
📝 https://doi.org/10.7554/eLife.110277
#Neuroscience #CompNeuro #NeuralCircuits #Imaging @eLife https://fediscience.org/@eLife/116589668668928682
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🧠 New preprint by Kim et al. (2025) from David Anderson’s lab: A line #attractor maintains aggressiveness during feeding in “hangry” mice 🍔🐁. Using in vivo #CalciumImaging and #rSLDS modeling, they show how moderate fasting stabilizes an aggression-related attractor in #VMHvl, while prolonged fasting collapses it, linking hunger, motivation, and aggression through #PopulationDynamics:
🌍 https://doi.org/10.1101/2025.10.16.682711
#Neuroscience #CompNeuro #Behavior #AttractorDynamics #Hypothalamus #2p #imaging
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If you want to study #HippocampalReplay... Use ephys, not #CalciumImaging!!
(Calcium imaging doesn't detect single spikes well, but replay mostly involves single spikes)
#Neuroscience #SpatialCognition #Hippocampus -
If you want to study #HippocampalReplay... Use ephys, not #CalciumImaging!!
(Calcium imaging doesn't detect single spikes well, but replay mostly involves single spikes)
#Neuroscience #SpatialCognition #Hippocampus -
New #TeachingMaterial available: Functional Imaging Data Analysis – From Calcium Imaging to Network Dynamics. This course covers the entire workflow from raw #imaging data to functional insights, including #SpikeInference & #PopulationAnalysis. Designed for students and for self-guided learning, with a focus on open content and reproducibility. Feel free to use and share it 🤗
🌍 https://www.fabriziomusacchio.com/blog/2025-07-13-function_image_analysis/
#Python #DataScience #MachineLearning #Neuroscience #OpenSource #calciumimaging #CompNeuro
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📢 Our new study is now published in Communications Biology (Nature Portfolio):
We demonstrate deep in vivo #ThreePhoton imaging 🔬 of neurons 🧠 and glia in the medial prefrontal cortex with subcellular resolution!👉 https://www.nature.com/articles/s42003-025-08079-8
#Neuroscience #Microscopy #CalciumImaging #Microglia #DZNE @dzne
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📢Hot off the press: "Neuronal correlates of sleep in honey bees"
#CalciumImaging🔬 in sleeping #bees🐝: Antennal lobe neurons synchronise stronger during #sleep, likely due to reduced GABAergic coupling. #SNN💻 simulations show reduced #odour processing, similar to human sleep😴.
📰in Neural Networks: https://doi.org/10.1016/j.neunet.2025.107575
🍾Thanks to all collaborators: Sebastian Moguilner, Ettore Tiraboschi, Giacomo Fantoni, Heather Strelevitz, Hamid Soleimani, Luca Del Torre, @urihasson
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📢Hot off the press: "Neuronal correlates of sleep in honey bees"
#CalciumImaging🔬 in sleeping #bees🐝: Antennal lobe neurons synchronise stronger during #sleep, likely due to reduced GABAergic coupling. #SNN💻 simulations show reduced #odour processing, similar to human sleep😴.
📰in Neural Networks: https://doi.org/10.1016/j.neunet.2025.107575
🍾Thanks to all collaborators: Sebastian Moguilner, Ettore Tiraboschi, Giacomo Fantoni, Heather Strelevitz, Hamid Soleimani, Luca Del Torre, @urihasson
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Quite the big deal:
"Light-field deep learning enables high-throughput, scattering-mitigated calcium imaging", by Howe et al. 2025 (Amanda Foust lab).
https://www.biorxiv.org/content/10.1101/2025.03.17.643718v1.fullTransfers one-photon light field images of Ca2+ sensors monitoring neuronal activity, which suffer from scattering in the mouse brain, to two-photon volumes that don't, using machine learning.
Image volumes acquired at 100 Hz demonstrate 10Hz spike rates.
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Quite the big deal:
"Light-field deep learning enables high-throughput, scattering-mitigated calcium imaging", by Howe et al. 2025 (Amanda Foust lab).
https://www.biorxiv.org/content/10.1101/2025.03.17.643718v1.fullTransfers one-photon light field images of Ca2+ sensors monitoring neuronal activity, which suffer from scattering in the mouse brain, to two-photon volumes that don't, using machine learning.
Image volumes acquired at 100 Hz demonstrate 10Hz spike rates.
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"Forecasting Whole-Brain Neuronal Activity from Volumetric Video", Immer et al. 2025 (with Florian Engert, Jeff Lichtman, Misha Ahrens, Viren Jain and Michal Januszewski)
https://www.arxiv.org/abs/2503.00073"ZAPBench: a benchmark for whole-brain activity prediction in zebrafish", Lueckmann et al. 2025
https://openreview.net/pdf?id=oCHsDpyawq#ZAPBench #neuroscience #zebrafish #CalciumImaging #CompNeurosci
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"Forecasting Whole-Brain Neuronal Activity from Volumetric Video", Immer et al. 2025 (with Florian Engert, Jeff Lichtman, Misha Ahrens, Viren Jain and Michal Januszewski)
https://www.arxiv.org/abs/2503.00073"ZAPBench: a benchmark for whole-brain activity prediction in zebrafish", Lueckmann et al. 2025
https://openreview.net/pdf?id=oCHsDpyawq#ZAPBench #neuroscience #zebrafish #CalciumImaging #CompNeurosci
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Comparative study between D. melanogaster and the invasive D. suzukii. Significant differences in structure and function of the antennal lobes could be the basis for their different host-seeking behaviour causing huge crop damage: https://www.mdpi.com/2075-4450/16/1/84
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Comparative study between D. melanogaster and the invasive D. suzukii. Significant differences in structure and function of the antennal lobes could be the basis for their different host-seeking behaviour causing huge crop damage: https://www.mdpi.com/2075-4450/16/1/84
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New preprint with @urihasson : https://biorxiv.org/cgi/content/short/2024.10.11.617548v1
First #calciumimaging of the #honeybee brain during #sleep.
#Machinelearning distinguishes sleep from wakefulness with 93% accuracy in #olfactory network. Clearest difference: the #neuralnetwork state. Nodes are more synchronized during sleep.
A simulation shows reduced inhibitory coupling during sleep, meaning less information processing. Increased inhibition during wakefulness leads to highly distinguishable odour maps. #CIMeC #UniTrento -
New preprint with @urihasson : https://biorxiv.org/cgi/content/short/2024.10.11.617548v1
First #calciumimaging of the #honeybee brain during #sleep.
#Machinelearning distinguishes sleep from wakefulness with 93% accuracy in #olfactory network. Clearest difference: the #neuralnetwork state. Nodes are more synchronized during sleep.
A simulation shows reduced inhibitory coupling during sleep, meaning less information processing. Increased inhibition during wakefulness leads to highly distinguishable odour maps. #CIMeC #UniTrento -
The Schreiter lab did it again:
"A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging", Helen Farrants et al. 2024
https://www.nature.com/articles/s41592-024-02411-6"WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan."
I'll have to update my lectures on optogenetics and chemigenetics ...
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The Schreiter lab did it again:
"A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging", Helen Farrants et al. 2024
https://www.nature.com/articles/s41592-024-02411-6"WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan."
I'll have to update my lectures on optogenetics and chemigenetics ...
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Commentary of:
"Aberrant hippocampal Ca2+ micro-waves following synapsin-dependent adeno-associated viral expression of Ca2+ indicators" by Masala et al. 2024.
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Commentary of:
"Aberrant hippocampal Ca2+ micro-waves following synapsin-dependent adeno-associated viral expression of Ca2+ indicators" by Masala et al. 2024.
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@moritz_negwer I haven't read this preprint but I wouldn't be surprised to know that heating changes the brain activity since all/most of the proteins would be affected by heat?
It reminded me of this paper from 2016: Brain heating induced by near-infrared lasers during multiphoton microscopy where they used thermocouple probes and quantum dot nanothermometers to measure temperature changes induced by 2-photon microscopy in the neocortex of awake and anaesthetized mice
From the abstract
"Although total power is highest near the surface of the brain, heating was most severe hundreds of micrometers below the focal plane, due to heat dissipation through the cranial window. Continuous illumination of a 1-mm2 area produced a peak temperature increase of ∼1.8°C/100 mW. Continuous illumination with powers above 250 mW induced lasting damage, detected with immunohistochemistry against Iba1, glial fibrillary acidic protein, heat shock proteins, and activated caspase-3. Higher powers were usable in experiments with limited duty ratios, suggesting an approach to mitigate damage in high-power microscopy experiments."
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@moritz_negwer I haven't read this preprint but I wouldn't be surprised to know that heating changes the brain activity since all/most of the proteins would be affected by heat?
It reminded me of this paper from 2016: Brain heating induced by near-infrared lasers during multiphoton microscopy where they used thermocouple probes and quantum dot nanothermometers to measure temperature changes induced by 2-photon microscopy in the neocortex of awake and anaesthetized mice
From the abstract
"Although total power is highest near the surface of the brain, heating was most severe hundreds of micrometers below the focal plane, due to heat dissipation through the cranial window. Continuous illumination of a 1-mm2 area produced a peak temperature increase of ∼1.8°C/100 mW. Continuous illumination with powers above 250 mW induced lasting damage, detected with immunohistochemistry against Iba1, glial fibrillary acidic protein, heat shock proteins, and activated caspase-3. Higher powers were usable in experiments with limited duty ratios, suggesting an approach to mitigate damage in high-power microscopy experiments."
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It's long been known that cooling a brain region reduces activity. But this #preprint claims that the reverse is also true: pulsed infrared light (1875nm) from a glass fiber locally heating neurons can change their activity. Data looks noisy but this might be interesting if true. (Inclusion into optrodes maybe?)
Two-photon imaging of excitatory and inhibitory neural response to infrared neural stimulation
Fu et al., biorxiv preprint 2024
https://www.biorxiv.org/content/10.1101/2024.02.28.582632v1 -
It's long been known that cooling a brain region reduces activity. But this #preprint claims that the reverse is also true: pulsed infrared light (1875nm) from a glass fiber locally heating neurons can change their activity. Data looks noisy but this might be interesting if true. (Inclusion into optrodes maybe?)
Two-photon imaging of excitatory and inhibitory neural response to infrared neural stimulation
Fu et al., biorxiv preprint 2024
https://www.biorxiv.org/content/10.1101/2024.02.28.582632v1 -
@jbaert Lots of modern #invivo #neurobiology is done like this, conceptually. Swap the GPU for a brain and the microphone for a -scope, and this could be a neat "cell population dynamics of enemy perception in a virtual environment" #calciumimaging (or EEG?) study.
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@jbaert Lots of modern #invivo #neurobiology is done like this, conceptually. Swap the GPU for a brain and the microphone for a -scope, and this could be a neat "cell population dynamics of enemy perception in a virtual environment" #calciumimaging (or EEG?) study.
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Please welcome the great @aheadofthenerve to Mastodon / the Fediverse! So nice to have another #PlaceCell #Neuroscientist on here 😁 (and also a #CalciumImaging expert)!
From: @aheadofthenerve
https://neuromatch.social/@aheadofthenerve/111767478048631695 -
#FIOLA, new pipeline for processing #CalciumImaging or #VoltageImaging 🌌🔬data, including fast speed and online processing 👌
✍️ Cai, C., Dong, C., Friedrich, J. et al. FIOLA: an accelerated pipeline for fluorescence imaging online analysis. #NatMethods
🌍 https://doi.org/10.1038/s41592-023-01964-2 -
@elduvelle we are a Neurophysics lab at the University of Trento Italy and do two-photon #calciumimaging in insects.
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@elduvelle we are a Neurophysics lab at the University of Trento Italy and do two-photon #calciumimaging in insects.
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#CalciumImaging reveals the circuit mechanisms underlying embryonic #RetinalWaves in mice. #Neuroscience https://elifesciences.org/articles/81983?utm_source=mastodon&utm_medium=social&utm_campaign=organic
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#CalciumImaging reveals the circuit mechanisms underlying embryonic #RetinalWaves in mice. #Neuroscience https://elifesciences.org/articles/81983?utm_source=mastodon&utm_medium=social&utm_campaign=organic
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@elduvelle We are a #neuroscience lab and I consider myself a #neuroscientist. We do both #Ephys and #CalciumImaging in the lab, but I don't do it myself personally–I wish. At least I do some of the software programming, which I enjoy immensely.
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@elduvelle We are a #neuroscience lab and I consider myself a #neuroscientist. We do both #Ephys and #CalciumImaging in the lab, but I don't do it myself personally–I wish. At least I do some of the software programming, which I enjoy immensely.
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Hi! If you’re a #Neuroscientist who does #Ephys or #CalciumImaging can you make yourself known? I’ll add you to my list. 🧠⚡📃
(Unfortunately lists are not public here but I’ll happily share it, maybe once it’s grown a bit)
Edit: Please boost if you have relevant followers!
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Hi! If you’re a #Neuroscientist who does #Ephys or #CalciumImaging can you make yourself known? I’ll add you to my list. 🧠⚡📃
(Unfortunately lists are not public here but I’ll happily share it, maybe once it’s grown a bit)
Edit: Please boost if you have relevant followers!
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Are you interested in learning in vivo #calciumimaging and #optogenetics, combined with #behaviour #analysis? We are now accepting applications for our 2-week (4-15 Sep) intensive EMBO Practical Course LINdoscope: Neuroimaging and data analysis. APPLY NOW: https://meetings.embo.org/event/23-lindoscope#Register
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Are you interested in learning in vivo #calciumimaging and #optogenetics, combined with #behaviour #analysis? We are now accepting applications for our 2-week (4-15 Sep) intensive EMBO Practical Course LINdoscope: Neuroimaging and data analysis. APPLY NOW: https://meetings.embo.org/event/23-lindoscope#Register
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How do #bees respond to #geosmin, the #smell of rain and wet soil?
Great collaboration with Florencia Scarano, Mukilan Deivarajan, Ettore Tiraboschi, Amélie Cabirol, Morgane Nouvian, and @drtnowotny,
using #stinging assays, #electroantennography, #calciumimaging, and #snn simulations"Geosmin suppresses defensive behaviour and elicits unusual neural responses in honey bees" just published in Scientific Reports
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How do #bees respond to #geosmin, the #smell of rain and wet soil?
Great collaboration with Florencia Scarano, Mukilan Deivarajan, Ettore Tiraboschi, Amélie Cabirol, Morgane Nouvian, and @drtnowotny,
using #stinging assays, #electroantennography, #calciumimaging, and #snn simulations"Geosmin suppresses defensive behaviour and elicits unusual neural responses in honey bees" just published in Scientific Reports
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Doing this for #JournalClub soon:
Hippocampal representations of foraging trajectories depend upon spatial context
Did you read it?
Did you like it?#Hippocampus #CalciumImaging #VR #Joystick #RL #Optogenetics #Micr
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Doing this for #JournalClub soon:
Hippocampal representations of foraging trajectories depend upon spatial context
Did you read it?
Did you like it?#Hippocampus #CalciumImaging #VR #Joystick #RL #Optogenetics #Micr
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After years of perfecting my scrambled eggs technique, I am happy to report that our paper on optogenetic scrambling to dissociate spatiotemporal codes and memory is out in Nature Communications: https://doi.org/10.1038/s41467-023-35825-5 #hippocampus #CA1 #CalciumImaging #Miniscope #GCaMP #Optogenetics #Memory #InVivo #Electrophysiology #ThetaOscillations
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After years of perfecting my scrambled eggs technique, I am happy to report that our paper on optogenetic scrambling to dissociate spatiotemporal codes and memory is out in Nature Communications: https://doi.org/10.1038/s41467-023-35825-5 #hippocampus #CA1 #CalciumImaging #Miniscope #GCaMP #Optogenetics #Memory #InVivo #Electrophysiology #ThetaOscillations
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"NIT: an open-source tool for information theoretic analysis of neural population data"
https://www.biorxiv.org/content/10.1101/2022.12.11.519966v1#Neuroscience #Neuro #Brain #DataAnalysis #InformationTheory #TwoPhoton #CalciumImaging
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... We demonstrate this adaptable pipeline approach by comparing the #SlowWave dynamics across multiple #OpenAccess #ECoG and #CalciumImaging datasets of anesthetized mice. In this meta-analysis, we can identify the influences of experimental parameters such as the anesthetic type and dosage and the spatial resolution of the recording technique.
The pipeline development is #opensource (#Python) and is already being reused for other research applications. ...
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Hello world! The #Neurophysics Lab at the University of #Trento is now on Mastodon. We look forward to discussing about #Neuroscience, #QuantumBiology, #Olfaction, #Magnetoreception, #CalciumImaging, #Insects ...
https://r.unitn.it/en/cimec/nphys