z stacks consisting of 19 slices with 0.33 μm separation were captured using a GFP/mCherry filter set (Chroma 59022), with 50 ms exposure per slice per channel.
A z-stack of half of the coelomocyte was acquired at maximum speed (200 ms exposure per slice) with 0.2 µm spacing.
For the main fMRI experiment, a high-resolution (2.3 × 2.3 × 2.3 mm) echo-planar imaging (EPI) sequence with BOLD contrast (96×9696 matrix, echo time = 36 ms, acquisition time per slice = 85 ms, repetition time = 2.55, interleaved slice order) was used to acquire 30 near-axial slices, positioned to optimize coverage of the occipital lobe.
Repetition time was 4.05 s (90 ms per slice*45 slices).
The actual TR between segments was about 55 ms per segment per slice.
Note that all acquisitions used fat saturation pulses, which have a shared effect on multiple images in M-EPI, adding 13 ms, 3.2 ms, and 1.5 ms to the average time per slice for the 1×1, 2×2, and 3×3 accelerations (for the 3 mm resolutions), respectively.
The imaging parameters were as follows: TR/TE = 15/1.59 ms, slices per slab = 52, slice thickness = 3.0 mm, flip angle = 5° and 26°, matrix = 256 × 256, and FOV = 231 mm × 231 mm.
DTI was acquired using a single shot echo planar imaging sequence with the following parameters: b=750 s/mm; 12 diffusion directions repeated five times; 5 b0-values per slice, TR=6100 ms, TE=117 ms, number of slices: 30, slice thickness: 3 mm (gap 1.9 mm), in-plane resolution: 1.2×1.2 mm, bandwidth: 840 Hz/pixel.
For a participant with a heart rate of 60 beats per minute (or 1,000 ms per beat), 18 slices would be used, with a volume acquisition time of 1,800 ms and an acquisition window of 1,900 ms.
