Optimal Z-spacing follows Nyquist in Z: Δz ≤ axial_resolution / 2.3. For 1.1 NA at 525nm: axial resolution ~600nm, optimal Δz ~260nm. Total planes = Sample thickness / Δz. Data volume scales linearly with Z-planes. Acquisition time scales as Z × (exposure + overhead_per_plane).
Acquisition Parameter
Z-Planes
Slices through the sample
View
Definition
The number of focal planes captured in a Z-stack, determining the axial extent and resolution of 3D imaging. More planes provide finer Z-sampling and deeper coverage but increase acquisition time and data volume.
Technical Details
Simplified
Imagine slicing a loaf of bread—each slice is a Z-plane. More slices give you a complete picture of the whole loaf (your 3D sample). But more slices means more time slicing and more slices to look at.
Why It Matters
Fly brain Z-stacks typically require 400-500 planes to cover the sample thickness with adequate Z-sampling. This large plane count is why per-plane overhead matters so much—1 second of overhead × 500 planes = 8+ minutes of wasted time.
Practical Example
Cleared fly brain, ~150μm thick, with 300nm Z-spacing: 150/0.3 = 500 planes. At 100ms exposure with 5-camera system: ~50 seconds camera time. With filter wheel adding 5 seconds per plane: +2500 seconds = +42 minutes.