Fig. 3

Fly specimen. A,B Volume rendering (A) and orthogonal sections (B) of a 3D image of fly embryo taken around 24 h after puparium formation, covering a portion of the abdomen (showing histoblast cells and larval cells), and a portion of the developing wing. Scale bar 50 μm. Four surfaces of interest may be identified in the dataset (of dimensions 1200 × 1200 × 51 voxels): surfaces S1 and S2 are relatively close to one another and located within overlapping z-ranges (8 ≤ z ≤ 50 and 20 ≤ z ≤ 50, respectively). Surfaces S3 and S4 (located in the z-ranges 42 ≤ z ≤ 50 and 9 ≤ z ≤ 50, respectively) are relatively far from each other and can nearly be separated by a plane. C 3D representations of the height maps extracted by Zellige (in green) and of the ground truth height maps (GT, in blue) of surfaces S1–S4. The reconstructed height maps of all surfaces S1–S4 cover >93% of the area of the corresponding GT (cf. Additional file 3: Figure S2 and Additional file 1: Supplementary Table S1). To reduce the staircase artifacts (more or less visible depending on the surface) due to the digitization of the GT and reconstructed height maps, all height maps were smoothed with a 2D Gaussian filter with a standard radius of 5 pixels (cf. Additional file 1: Supplementary Note 1). D Error maps (color-coded distance along the z-axis between the reconstructed and the GT height maps) plotted for each of the reconstructed surfaces. The large majority of pixels on the reconstructed height maps (98%, 96%, 91%, and 99% for surfaces S1 to S4, respectively) display errors of <2 pixels. The height maps of surfaces S1, S2, S4 show subpixel accuracy on average (RMSE < 1), while that of surface S3 is slightly less accurate (RMSE = 1.25). E Projections of the 3D image localized to the different surfaces S1–S4 (in this and all subsequent figures, these are maximum intensity projections over a subvolume of width δz=±1 pixel above or below the corresponding height maps). Upper and lower panels show the projections based on the GT and the reconstructed height maps, respectively. Scale bar 50 μm