Light field microscopy setup and volumetric imaging in bright field and fluorescence: (a) Fluorescent light from the specimen is guided via a dichroic mirror and emission filter to a microlens array projecting it to different subregions of the plenoptic camera’s image sensor (reflectance images from white light illumination are captured without filters). (b) Reconstructed light field data obtained from a wild-type larva showing strong contrast from naturally present pigments in the eyes (red dashed outlines) and in the head region; (c) Corresponding depth information calculated from the light field data with most superficial structures shown in magenta and deeper structures in blue; (d) Raw grayscale image showing two fluorescence beads (1 µm in diameter, white and yellow arrows) embedded in an agar phantom projected onto the image sensor via microlenses with different focal lengths (red/green/blue circles label microlenses with close/medium/far focal lengths); and (d′) Three-dimensional visualization of the same two volumetrically reconstructed fluorescent spheres (white and yellow arrows).

Spatiotemporal patterns of neuronal responses to an aversive odor captured by light field microscopy: (a) Three transverse planes selected from the volumetric reconstruction of a single frame captured by the plenoptic camera showing fluorescence signals from the brain of a calcium reporter zebrafish larva (7-day-old HuC:GCaMP5g) during stimulation with the aversive odorant cadaverine; (b–b′) Corresponding top-down maximum intensity projection with a colored overlay of regions of interest (ROIs) automatically selected for their substantial fluorescent signal changes in response to cadaverine. The color indicates the clusters of ROIs with high correlation between their corresponding temporal signal profiles shown in (b’). Delivery of cadaverine occurred during the omitted time points (dark gray area labeled “cad”). The white broken lines indicate the peak fluorescence signal of the deep purple trace as a reference to appreciate the earlier responses in the yellow and green traces; (c–c′) Schematic drawings of the larval brain seen from dorsal (c) and lateral views (c′) also indicating the site where the odorant cadaverine (cad) was presented. OE: olfactory epithelium, OB: olfactory bulb, OT: optic tectum, and Hb: habenula. (d) Rendered imaging volume showing simultaneous imaging of neuronal activity (high counts from fluorescence shown on color scale) and tail movements (low counts shown on grayscale) in response to cadaverine stimulation [deflection of the tail’s axis from the dashed white line is shown for a second time point (t2)]. Clustered ROIs are shown on a top-down maximum intensity projection in the inset on the lower left and color-coded signal time courses are shown on the right. Tail deflections coincident with some neuronal activations are represented as gray bars.