Figure S2 Schematic diagram of tilt imaging system based on the linear X-ray PD array. (A) Overview of tilt imaging system showing left, right and centred PD elements of the linear X-ray PD array. A left-side PD element detects the left-tilt image of the sample, because the X-rays arriving at the detector are tilted to the left by the sample. Likewise, the right-side PD element detects the right-tilt images. (B) Schematic showing the influence of different detection angles on the detected length Pxi. The left-side PD located at h1 detects the EB-scanned width of Ex reduced by cos(h1), [Px1 = Excos(h1)]. The centre PD element (under the sample) detects the same width as the EB-scanned length, [Px2 = Ex]. (C) Schematic showing the angles of each X-ray PD element. The linear X-ray PD array is positioned 13 mm under the sample. Each PD element is a 265 mm2 rectangle, and there are seven active signal-detection elements from among the 16 elements. The angles between the EB-irradiated spot and the PD elements are 240.2u,228.1u,213.0u, 4.4u, 21.0u, 34.7u and 45.0u. (TIF) Figure S3 Outline of 3D mask calculation. First, the 2D X- ray-image masks are calculated with 2s larger than the image’s average intensity. The intensity of this 2D mask is normalized to range from 0 to 100. Each 2D mask is back projected onto the angle corresponding to the PD. The 3D mask is obtained from the References 1. Sali A, Glaeser R, Earnest T, Baumeister W (2003) From words to literature in structural proteomics. Nature 422: 216–225. 2. Meyer JC, Girit CO, Crommie MF, Zettl A (2008) Imaging and dynamics of light atoms and molecules on graphene. Nature 454: 319–322. 3. Koshino M, Tanaka T, Solin N, Suenaga K, Isobe H, et al. (2007) Imaging of single organic molecules in motion. Science 316: 853–853. 4. de Smit E, Swart I, Creemer JF, Hoveling GH, Gilles MK, et al. 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