Skip to content
DraconiticResearch
Search Sources API
203,234 studies31 sourcesUpdated 50 min ago
Peer-reviewedCC BYNature Methods

Spike inference from calcium imaging data acquired with GCaMP8 indicators

  • Peter Rupprecht1,2
  • Márton Rózsa3,4
  • Xusheng Fang5,6
  • Karel Svoboda3,4
  • Fritjof Helmchen5,7,8
8 affiliations
  1. 1Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Zurich, Switzerland. [email protected]
  2. 2Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland. [email protected]
  3. 3Allen Institute for Neural Dynamics, Seattle, WA, USA
  4. 4Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
  5. 5Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Zurich, Switzerland
  6. 6University of Turku, Turku, Finland
  7. 7Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
  8. 8University Research Priority Program (URPP), Adaptive Brain Circuits in Development and Learning, University of Zurich, Zurich, Switzerland
Open at sourcePDFDOICite

Abstract

Calcium imaging is a central method in neuroscience but it records neuronal activity only indirectly and thereby produces results that are difficult to interpret. Here we evaluate the GCaMP8 calcium indicator variants, together with methods to infer neuronal spiking, and thus interpret GCaMP8 recordings. We find that the linearity of GCaMP8 indicators enables accurate detection of both single action potentials and high-frequency spiking events. Ground-truth recordings from mouse neocortex show that the most linear variants GCaMP8s and GCaMP8m (but not GCaMP6, GCaMP7f or GCaMP8f) robustly detect isolated spikes in cortical pyramidal neurons. In addition, we fine-tune and benchmark algorithms for spike inference (CASCADE, OASIS and MLSpike) with data from all GCaMP8 variants for pyramidal neurons and interneurons, and we demonstrate how the fast rise time of GCaMP8 indicators enables real-time detection of neuronal activity. Overall, we provide tools and guidelines to optimally process GCaMP8 calcium signals and highlight the key role of linearity in interpreting calcium imaging data.

Related

  1. Combining membrane potential and calcium imaging in brain slices using the voltage-sensitive dye ElectroFluor630 and the calcium indicator Calbryte520
    Shirin Ghasemiform, Marco Canepari
    NeurophotonicsPeer-reviewedCC BY1 citedBiophysicsHAL
  2. Calcium-independent biosensors for multiplexed in vivo imaging of extracellular lactate dynamics
    J.-J. Liu, H. Mizuno, E. Than-Trong +15
    bioRxivPreprintCC BY-NC-NDFull textMolecular biology & gene regulationbioRxiv
  3. Rapid volumetric reconstruction and tracking for Fourier light-field microscopy enables real-time calcium imaging in freely behaving Hydra.
    R. Adkins, R. Hausen, J. Noss +2
    bioRxivPreprintCC BYFull textBiophysicsbioRxiv
  4. CalciSeg : A versatile approach for unsupervised segmentation of calcium imaging data
    Marco Paoli, Yuri Antonacci, Angela Albi +2
    NeuroImagePeer-reviewedCC BY-NC-ND4 citedBiophysicsHAL
  5. Acquired epithelial Wnt7b secretion establishes autocrine WNT dependency in BRAF mutant colorectal cancer
    S. R. Lampart, T. Khadam-Al-Jame, P. Leary +7
    bioRxivPreprintAll rights reservedFull textMolecular biology & gene regulationbioRxiv

Cite

BibTeXRIS
BibTeX
@article{rupprecht2026spike,
  title = {{Spike inference from calcium imaging data acquired with GCaMP8 indicators}},
  author = {Peter Rupprecht and Márton Rózsa and Xusheng Fang and Karel Svoboda and Fritjof Helmchen},
  journal = {Nature Methods},
  year = {2026},
  month = jul,
  doi = {10.1038/s41592-026-03183-x},
  url = {https://doi.org/10.1038/s41592-026-03183-x},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Spike inference from calcium imaging data acquired with GCaMP8 indicators
AU  - Peter Rupprecht
AU  - Márton Rózsa
AU  - Xusheng Fang
AU  - Karel Svoboda
AU  - Fritjof Helmchen
PY  - 2026
DA  - 2026/07/27
JO  - Nature Methods
DO  - 10.1038/s41592-026-03183-x
UR  - https://doi.org/10.1038/s41592-026-03183-x
AB  - Calcium imaging is a central method in neuroscience but it records neuronal activity only indirectly and thereby produces results that are difficult to interpret. Here we evaluate the GCaMP8 calcium indicator variants, together with methods to infer neuronal spiking, and thus interpret GCaMP8 recordings. We find that the linearity of GCaMP8 indicators enables accurate detection of both single action potentials and high-frequency spiking events. Ground-truth recordings from mouse neocortex show that the most linear variants GCaMP8s and GCaMP8m (but not GCaMP6, GCaMP7f or GCaMP8f) robustly detect isolated spikes in cortical pyramidal neurons. In addition, we fine-tune and benchmark algorithms for spike inference (CASCADE, OASIS and MLSpike) with data from all GCaMP8 variants for pyramidal neurons and interneurons, and we demonstrate how the fast rise time of GCaMP8 indicators enables real-time detection of neuronal activity. Overall, we provide tools and guidelines to optimally process GCaMP8 calcium signals and highlight the key role of linearity in interpreting calcium imaging data.
SN  - 1548-7091
SN  - 1548-7105
ER  -