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El Duvelle NeuroIf you want to study <a href="https://neuromatch.social/tags/HippocampalReplay" class="mention hashtag" rel="nofollow noopener" target="_blank">#HippocampalReplay</a>... Use ephys, not <a href="https://neuromatch.social/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a>!!(Calcium imaging doesn't detect single spikes well, but replay mostly involves single spikes) <a href="https://neuromatch.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscience</a> <a href="https://neuromatch.social/tags/SpatialCognition" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpatialCognition</a> <a href="https://neuromatch.social/tags/Hippocampus" class="mention hashtag" rel="nofollow noopener" target="_blank">#Hippocampus</a>

Fabrizio MusacchioNew <a href="https://sigmoid.social/tags/TeachingMaterial" class="mention hashtag" rel="nofollow noopener" target="_blank">#TeachingMaterial</a> available: Functional Imaging Data Analysis – From Calcium Imaging to Network Dynamics. This course covers the entire workflow from raw <a href="https://sigmoid.social/tags/imaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#imaging</a> data to functional insights, including <a href="https://sigmoid.social/tags/SpikeInference" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpikeInference</a> & <a href="https://sigmoid.social/tags/PopulationAnalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#PopulationAnalysis</a>. Designed for students and for self-guided learning, with a focus on open content and reproducibility. Feel free to use and share it 🤗🌍 <a href="https://www.fabriziomusacchio.com/blog/2025-07-13-function_image_analysis/" rel="nofollow noopener" translate="no" target="_blank">https://www.fabriziomusacchio.com/blog/2025-07-13-function_image_analysis/</a> <a href="https://sigmoid.social/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#Python</a> <a href="https://sigmoid.social/tags/DataScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#DataScience</a> <a href="https://sigmoid.social/tags/MachineLearning" class="mention hashtag" rel="nofollow noopener" target="_blank">#MachineLearning</a> <a href="https://sigmoid.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscience</a> <a href="https://sigmoid.social/tags/OpenSource" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenSource</a> <a href="https://sigmoid.social/tags/calciumimaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#calciumimaging</a> <a href="https://sigmoid.social/tags/CompNeuro" class="mention hashtag" rel="nofollow noopener" target="_blank">#CompNeuro</a>

Fabrizio Musacchio📢 Our new study is now published in Communications Biology (Nature Portfolio): We demonstrate deep in vivo <a href="https://sigmoid.social/tags/ThreePhoton" class="mention hashtag" rel="nofollow noopener" target="_blank">#ThreePhoton</a> imaging 🔬 of neurons 🧠 and glia in the medial prefrontal cortex with subcellular resolution!👉 <a href="https://www.nature.com/articles/s42003-025-08079-8" rel="nofollow noopener" translate="no" target="_blank">https://www.nature.com/articles/s42003-025-08079-8</a><a href="https://sigmoid.social/tags/Neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscience</a> <a href="https://sigmoid.social/tags/Microscopy" class="mention hashtag" rel="nofollow noopener" target="_blank">#Microscopy</a> <a href="https://sigmoid.social/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a> <a href="https://sigmoid.social/tags/Microglia" class="mention hashtag" rel="nofollow noopener" target="_blank">#Microglia</a> <a href="https://sigmoid.social/tags/DZNE" class="mention hashtag" rel="nofollow noopener" target="_blank">#DZNE</a> <a href="https://social.bund.de/@dzne" class="u-url mention" rel="nofollow noopener" target="_blank">@dzne</a>

Albert CardonaQuite the big deal:"Light-field deep learning enables high-throughput, scattering-mitigated calcium imaging", by Howe et al. 2025 (Amanda Foust lab). <a href="https://www.biorxiv.org/content/10.1101/2025.03.17.643718v1.full" rel="nofollow noopener" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2025.03.17.643718v1.full</a>Transfers 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.<a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/mouse" class="mention hashtag" rel="nofollow noopener" target="_blank">#mouse</a> <a href="https://mathstodon.xyz/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a>

Albert Cardona"Forecasting Whole-Brain Neuronal Activity from Volumetric Video", Immer et al. 2025 (with Florian Engert, Jeff Lichtman, Misha Ahrens, Viren Jain and Michal Januszewski) <a href="https://www.arxiv.org/abs/2503.00073" rel="nofollow noopener" translate="no" target="_blank">https://www.arxiv.org/abs/2503.00073</a>"ZAPBench: a benchmark for whole-brain activity prediction in zebrafish", Lueckmann et al. 2025 <a href="https://openreview.net/pdf?id=oCHsDpyawq" rel="nofollow noopener" translate="no" target="_blank">https://openreview.net/pdf?id=oCHsDpyawq</a><a href="https://mathstodon.xyz/tags/ZAPBench" class="mention hashtag" rel="nofollow noopener" target="_blank">#ZAPBench</a> <a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/zebrafish" class="mention hashtag" rel="nofollow noopener" target="_blank">#zebrafish</a> <a href="https://mathstodon.xyz/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a> <a href="https://mathstodon.xyz/tags/CompNeurosci" class="mention hashtag" rel="nofollow noopener" target="_blank">#CompNeurosci</a>

Albert CardonaThe Schreiter lab did it again:"A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging", Helen Farrants et al. 2024 <a href="https://www.nature.com/articles/s41592-024-02411-6" rel="nofollow noopener" translate="no" target="_blank">https://www.nature.com/articles/s41592-024-02411-6</a>"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 ...<a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a> <a href="https://mathstodon.xyz/tags/WHaloCaMP" class="mention hashtag" rel="nofollow noopener" target="_blank">#WHaloCaMP</a>

Albert Cardona<a href="https://mastodon.social/@thetransmitter" class="u-url mention" rel="nofollow noopener" target="_blank">@thetransmitter</a> <a href="https://mastodon.social/@avaskham" class="u-url mention" rel="nofollow noopener" target="_blank">@avaskham</a> Commentary of:"Aberrant hippocampal Ca2+ micro-waves following synapsin-dependent adeno-associated viral expression of Ca2+ indicators" by Masala et al. 2024.<a href="https://elifesciences.org/reviewed-preprints/93804v2" rel="nofollow noopener" translate="no" target="_blank">https://elifesciences.org/reviewed-preprints/93804v2</a><a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#neuroscience</a> <a href="https://mathstodon.xyz/tags/GCaMP" class="mention hashtag" rel="nofollow noopener" target="_blank">#GCaMP</a> <a href="https://mathstodon.xyz/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a> <a href="https://mathstodon.xyz/tags/artifacts" class="mention hashtag" rel="nofollow noopener" target="_blank">#artifacts</a>

Fabrizio Musacchio<a href="https://sigmoid.social/tags/FIOLA" class="mention hashtag" rel="nofollow noopener" target="_blank">#FIOLA</a>, new pipeline for processing <a href="https://sigmoid.social/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a> or <a href="https://sigmoid.social/tags/VoltageImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#VoltageImaging</a> 🌌🔬data, including fast speed and online processing 👌✍️ Cai, C., Dong, C., Friedrich, J. et al. FIOLA: an accelerated pipeline for fluorescence imaging online analysis. <a href="https://sigmoid.social/tags/NatMethods" class="mention hashtag" rel="nofollow noopener" target="_blank">#NatMethods</a> 🌍 <a href="https://doi.org/10.1038/s41592-023-01964-2" rel="nofollow noopener" target="_blank">https://doi.org/10.1038/s41592-023-01964-2</a> <a href="https://sigmoid.social/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#neuroscience</a>

NeurophysicsLab Albrecht Haase<a href="https://neuromatch.social/@elduvelle" class="u-url mention" rel="nofollow noopener" target="_blank">@elduvelle</a> we are a Neurophysics lab at the University of Trento Italy and do two-photon <a href="https://mastodon.online/tags/calciumimaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#calciumimaging</a> in insects.

Albert Cardona<a href="https://neuromatch.social/@elduvelle" class="u-url mention" rel="nofollow noopener" target="_blank">@elduvelle</a> We are a <a href="https://mathstodon.xyz/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#neuroscience</a> lab and I consider myself a <a href="https://mathstodon.xyz/tags/neuroscientist" class="mention hashtag" rel="nofollow noopener" target="_blank">#neuroscientist</a>. We do both <a href="https://mathstodon.xyz/tags/Ephys" class="mention hashtag" rel="nofollow noopener" target="_blank">#Ephys</a> and <a href="https://mathstodon.xyz/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a> 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.

El DuvelleHi! If you’re a <a href="https://neuromatch.social/tags/Neuroscientist" class="mention hashtag" rel="nofollow noopener" target="_blank">#Neuroscientist</a> who does <a href="https://neuromatch.social/tags/Ephys" class="mention hashtag" rel="nofollow noopener" target="_blank">#Ephys</a> or <a href="https://neuromatch.social/tags/CalciumImaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#CalciumImaging</a> 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!

LINdoscopeAre you interested in learning in vivo <a href="https://masto.ai/tags/calciumimaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#calciumimaging</a> and <a href="https://masto.ai/tags/optogenetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#optogenetics</a>, combined with <a href="https://masto.ai/tags/behaviour" class="mention hashtag" rel="nofollow noopener" target="_blank">#behaviour</a> <a href="https://masto.ai/tags/analysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#analysis</a>? We are now accepting applications for our 2-week (4-15 Sep) intensive EMBO Practical Course LINdoscope: Neuroimaging and data analysis. APPLY NOW: <a href="https://meetings.embo.org/event/23-lindoscope#Register" rel="nofollow noopener" target="_blank">https://meetings.embo.org/event/23-lindoscope#Register</a>

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