How flat is your sample? An opportunistic survey of 3D tilt in public fluorescence microscopy data (opens in new tab)

Sample planarity is rarely monitored in fluorescence microscopy quality control, yet focal plane deviations across the field of view are a potential source of measurement error. Here I describe FlatStat, a tool that estimates sample tilt automatically from any 3D fluorescence stack, without prior knowledge of sample content, by fitting a plane to the Z-map of maximum intensity. Applied to an Argolight calibration slide and biological samples on a laser-scanning confocal system, FlatStat yield...