This PDF file includes:

• section S1. Derivation of T2S model
  
• section S2. Computational tractability
  
• section S3. Model calibration
  
• section S4. Gradient direction for iterative optimization
  
• section S5. MURA: A separable pattern
  
• section S6. FlatCam model: An approximation to the T2S model
  
• section S7. Diffraction effects and T2S model
  
• section S8. Light collection
  
• section S9. Impact of sensor saturation
  
• fig. S1. Calibration setup.
  
• fig. S2. Digital focusing.
  
• fig. S3. Simulation comparison of bare sensor, FlatScope, and FlatCam.
  
• fig. S4. 3D volume reconstruction accuracy.
  
• fig. S5. Fabrication of FlatScope.
  
• fig. S6. Refractive index matching.
  
• fig. S7. T2S derivation.
  
• fig. S8. Aberration removal using RPCA.
  
• fig. S9. Removing effects from autofluorescence.
  
• fig. S10. T2S model error from diffraction.
  
• fig. S11. Light collection comparison of FlatScope and microscope objectives.
  
• Legends for movies S1 and S2

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Other Supplementary Material for this manuscript includes the following:

• movie S1 (.mp4 format). Digital focusing of simulated resolution target.
  
• movie S2 (.mp4 format). Fluorescent beads flowing in microfluidic channels of different depths.