An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
Fig 2
Detection of ROIs corresponding to single neurons.
Four examples from different animal models, brain regions, imaging techniques and calcium indicators. Left: imaged optical planes. Perimeters of correct and incorrect automatically detected ROIs are shown in green and red, respectively. Yellow perimeters, detected ROIs that had to be manually curated, or undetected but manually drawn. Right: representative ΔF/F0 traces (black) and significant fluorescent transients detected (red). (A) Mouse primary visual cortex bolus injected with OGB-1 AM (two-photon imaging, 256x256 pixels, 30 Hz sampling rate). Data from Scholl et al[37]. Segmentation was performed with the “labeled nuclei” and “bigger ROI” options, and we set parameters “local contrast” to ~20 for spatial normalization of the image, thrneuropil and thrsoma to ~0.45 and ~0.095, respectively, and “minimal ROI area” to 18 pixels. (B) Mouse somatosensory cortex, where nuclei of excitatory neurons are transgenically labeled with mCherry (two-photon imaging, 256x256 pixels, 7 Hz sampling rate). Calcium dynamics monitored with GCaMP6s. Data from Peron et al[11,38]. Parameters used: “labeled nuclei” and “bigger ROI” options, “local contrast” ~43, thrneuropil ~0.15, thrsoma ~0.08, and “minimal ROI area” set to 15 pixels. (C) Transgenic zebrafish larva pan-neuronally expressing GCaMP3 (two-photon imaging, 512x256 pixels, 1 Hz sampling rate). Parameters used: “unlabeled nuclei” and “smaller ROI options”, “local contrast” ~10, thrneuropil ~0.15, thrsoma ~0.01, “minimal” and “maximal ROI areas” set to 7 and 40 pixels, and “minimal” and “maximal circularity” to ~0.48 and ~1.7. (D) Right hemisphere of the optic tectum of a transgenic zebrafish larva pan-neuronally expressing GCaMP5 (single-photon light-sheet imaging, 232x242 pixels, 100 Hz sampling rate). Parameters used: “unlabeled nuclei” and “smaller ROI options”, “local contrast” ~20, thrneuropil ~0.15, thrsoma ~0.01, “minimal ROI areas” set to 8 pixels.