Computationally Enhanced Quantitative Phase Microscopy

Toolbox for the ceQPM method

The ceQPM.m is an example script to process the QPM images acquired by the SID4BIO camera using the ceQPM method developed by Xili Liu, et al. The method is described in Liu, Xili, et al. "Computationally Enhanced Quantitative Phase Microscopy Reveals Autonomous Oscillations in Mammalian Cell Growth." bioRxiv (2019): 631119.

The image processing pipeline includes:
1. load the experiment information
2. make the synthetic reference image from the central FOVs
3. test the performance the reference by one FOV
4. apply the reference to all the images
5. remove additional background by the thin plate interpolation
6. process the fluorescent images
7. cell segmentation
8. cell tracking
9. save example FOVs

Since the processing pipeline varies with the experimental setting, we only give one example on how to process the time-lapse movie taken at multiple positions with multiple channels in a multiple-well plate (t_xy_c). And as such a QPM movie is usually very large, we do not include an example movie in the package. But the functions have been tested by other users with their own data.

The background removal parameters are sensitive to the magnification and cell area. The segmentation and tracking parameters are sensitive to the cell line. The parameters used in the example are specific for HeLa cells measured under the 10X objective.

For clarification, we only include the functions called by the example script in this package. One can easily modify the example functions to work for other experimental settings. Functions for other experimental settings or other cell lines are also available upon request.

Created by Xili Liu
Last modified on 4/21/2020
contact information: [e-mail]

This toolbox uses the array_padd function developed by Sergei Koptenko; imOverlay developed by David Legland; parseXML; parseChlidNodes; real2rgb and rescale developed by Oliver.Woodford.