QPI project overview

This part describe my research project which I use quantitative phase image method to record the motion of red blood cell flow in side microfludic device

Here I briefly shows the process and the result, 
check out the sidebar on the left for detail and the links to source code

Optical setup

Segmentation

• Using ICnet to detect to pisition of red blood cell for each frame

• Track the bounding box and seperate each cell

  

Phase retrieval, Refocus and Realign

• In QPI we use interferogram to store the phase delay cause by different sample. Therefore, an algorithm is needed to retrieve the quantitative information

• After retrieval, an numerical refocus algorithm is using to calibrate the focus distance change during cell motion

• Then I align all frames belong to each cell using center of mass, also unified the size and orientation of every frames

  

Angle calculation

• In order to do the three dimentional reconstruction, the representation angle of each frame should be estimate
• With uniform distribution, RBC can be seen as biolens and estimate its angle using Zernike polynomials which are used to describe wavefront aberrations
• Here I use differnt order to discribe different angle
  • Horizontal secondary astigmatism for 90 degree estimation
  • Defocus + Primary spherical abberation for 0 degree estimation
  • Defocus + Horizontal for other frame between each section of 0~90

3D reconstruction

• We use Fourier diffraction theory to do the reconstruction by mapping the frequency domain of each frame to 3d fourier space
• TVmin and constraint are add to the result to remove artifact