Nov 02, 2021
Spike Detection
- Bryan Yoo1,
- Jessica Griffiths1,
- Sarkis Mazmanian1
- 1California Institute of Technology
- Mazmanian Lab
Protocol Citation: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian 2021. Spike Detection . protocols.io https://dx.doi.org/10.17504/protocols.io.bzp9p5r6
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it’s working
Created: November 02, 2021
Last Modified: November 02, 2021
Protocol Integer ID: 54753
Funders Acknowledgements:
Center for Environmental and Microbial Interactions (CEMI)
Grant ID: n/a
Emerald Foundation
Grant ID: n/a
Heritage Medical Research Institute
Grant ID: n/a
National Institutes of Health
Grant ID: GM007616 and DK078938
Department of Defense
Grant ID: PD160030
Aligning Science Across Parkinson’s
Grant ID: ASAP-00037
Abstract
Protocol for spike detection of GCaMP6F imaging data used in Yoo et al 2021
Data sets of fluorescent values recorded at a rate of 0.206 s from GCaMP6F-expressing unstimulated neurons in the myenteric plexus of the proximal large intestine and analyzed with the MLspike software for Matlab downloaded from GitHub (https://github.com/MLspike/spikes) (Deneux et al., 2016).
MLspike determines a new baseline to subtract from the raw fluorescence data to allow accurate modelling. The software uses a version of the Viterbi algorithm to obtain the most probable spike train. From the model, fluctuating baseline, model-estimated spike train, and most probable spike times were extracted. Polynomial coefficients (p2) were changed from 0.5 to 0.55 and (p3) from 0.01 to 0.03 for GCaMP6F fluorescence as recommended (Deneux et al., 2016). The minimum range for baseline (bmin) was changed from 0.7 to 0.5 as determined by observed fluorescence values.