An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
Fig 8
Neuronal assemblies obtained using whole-brain light-sheet imaging in zebrafish reveals the spatial structure of brain activity.
A GCaMP5-expressing larva was volumetrically scanned with fast multi-plane single-photon light-sheet microscopy. Due to the lack of single-neuron resolution in this imaging dataset, a grid of 9 μm-diameter hexagons was imposed over each imaged optical plane. (A-F) Some of the ROI assemblies found with the PCA-promax method, displayed over the maximal intensity projection of all imaged optical sections (for individual optical sections see S2 Video). (A-D) Pairs of symmetric unilateral assemblies. (E-F) Single bilaterally symmetric assemblies. (G) All ROI assemblies found with the PCA-promax approach, displayed over the maximal intensity projection of all imaged optical sections (for individual optical sections see S3 Video). Assemblies are colored according to the similarity of their activity dynamics (the more temporally correlated, the more similar the color of the assemblies). This color code was also used in the previous panels (except for the assembly pair shown in c, which was colored differently to facilitate visualization). (H) Same as G, but for assemblies found using k-means, color-coded according to the similarity of their activity dynamics. To allow for a comparison between G and H, the dimensionality of the dataset was reduced through PCA before clustering (otherwise, clustering did not converge). Note how this clustering reveals assemblies whose spatial organization is roughly consistent with those shown in G, but exposes a much less biologically relevant fine structure. (I) Single-trial activation dynamics of the assemblies shown in D during one of the blocks of visual stimulation. Periods of moving-grating stimulation are labeled in red, angles indicate the grating's moving directions. Note that both assemblies are activated by this OMR-inducing stimulation, with the bluish and greenish assemblies preferring 60° and -60°, respectively.