Fig. 1
OPT and ALMOST imaging modalities. a Diagram of the imaging light path for a sample (green orb) with back illumination. b Theory of image formation in a tomographic system like OPT. The sample object resides at the center of a coordinate system. Parallel beams spaced by r pass through the sample to form a projected image (Pθ). The theory of this imaging process is based on the Radon transform (see also Additional file 1: Text S1 for more detailed background; r is used in the CT imaging and is less relevant for light-based approaches). c Diagram of the oblique illumination light path to create reflected light images of opaque samples, while standard OPT works with transparent samples and uses fluorescence or back illumination. It is also possible to add color filters in the reflected light path to collect spectral information. d Theory of image formation when reflected light interacts with an opaque sample that contains surface topography information. e The oblique illumination/imaging chamber for reflected light imaging is depicted. It is crucial to use a reflective chamber, for example, lined with white paper, to promote diffuse illumination. f Depiction of diffuse reflection compared to specular reflection. g, h Flowcharts of the imaging, reconstruction, and visualization process. The filtered back projection algorithm is abbreviated as filtered BPA. It is of note that if NRecon is used for reconstruction that the images are converted and need to be inverted back (see Additional file 1: Text S1 for more information)