Optical Diffraction Tomography (ODT)

HL60 HL60

Optical diffraction tomography (ODT) uses quantitative phase imaging techniques that record phase and intensity data (left image) of a cell from multiple angles to obtain the spatially resolved 3D refractive index of that cell (right image). I am interested in investigating single cells on the subcellular scale. ODT allows this in a marker-free manner and introduces the spatially-varying refractive index of biological cells as a structural marker. In the GuckLab, we measure the refractive using ODT in the Rytov approximation. In the course of this project, I have written several Python libraries that we are using for pre-processing and tomographic reconstruction of single cells:

  • ODTbrain: diffraction tomography with the Born and Rytov approximations
  • nrefocus: numerical focusing (refocusing, autofocusing) of complex wave fields
  • radontea: classical tomography with the inverse Radon transform
  1. P. Müller, “Optical Diffraction Tomography for Single Cells,” (PhD thesis, TU Dresden), 2016. url:http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-202261.  PDF 
  2. M. Schürmann, J. Scholze, P. Müller, J. Guck, and C. J. Chan, “Cell nuclei have lower refractive index and mass density than cytoplasm,” Journal of Biophotonics : 1068–1076, 2016. doi:10.1002/jbio.201500273.  PDF 
  3. P. Müller, M. Schürmann, C. J. Chan, and J. Guck, “Single-cell diffraction tomography with optofluidic rotation about a tilted axis,” Proc. of SPIE 9548: 95480U, 2015. doi:10.1117/12.2191501.
  4. P. Müller, M. Schürmann, and J. Guck, “ODTbrain: a Python library for full-view, dense diffraction tomography,” BMC Bioinformatics 16(1) : 1–9, 2015. doi:10.1186/s12859-015-0764-0.  PDF 
  5. P. Müller, M. Schürmann, and J. Guck, “The Theory of Diffraction Tomography.” 2015. arXiv:1507.00466 [q-bio.QM].  PDF 
  6. M. Schürmann, J. Scholze, P. Müller, C. J. Chan, A. E. Ekpenyong, K. J. Chalut, and J. Guck, “Refractive index measurements of single, spherical cells using digital holographic microscopy,” in Biophysical Methods in Cell Biology, 125, ed Ewa K. Paluch (Academic Press, 143–159), 2015. doi:10.1016/bs.mcb.2014.10.016.

Fluorescence Correlation Spectroscopy (FCS)

PyCorrFit

I have developed two graphical end-user programs, PyCorrFit and PyScanFCS, for data analysis in fluorescence correlation spectroscopy (FCS). At the time I started working with FCS and needed to process and fit my own experimental data, it was quite difficult to keep track of all the results that I produced with qtiplot. Since I was working with Linux and partially with Windows, I started with the Python programming language which made easy to port the software to any operating system.

multipletau

In addition to these graphical programs, I have implemented a multiple-tau correlation algorithm for Python. Multipe-tau correlation is computed on a logarithmic scale (less data points are computed) and is thus much faster than conventional correlation.

Binaries of the programs are available at GitHub/FCS-analysis, at the python package index, and have also been debianized by Alexandre Mestiashvili. The initial development of these programs was done in the group of Petra Schwille and a lot of input came from Thomas Weidemann who was my mentor at that time:

  • multipletau: python multiple-tau correlation algorithm
  • PyCorrFit: data analysis and fitting software for fluorescence correlation spectroscopy
  • PyScanFCS: data evaluation in perpendicular line scanning FCS
  1. P. Müller, P. Schwille, and T. Weidemann, “PyCorrFit – generic data evaluation for fluorescence correlation spectroscopy,” Bioinformatics , 2014. doi:10.1093/bioinformatics/btu328.  PDF 
  2. P. Müller, P. Schwille, and T. Weidemann, “Scanning fluorescence correlation spectroscopy (SFCS) with a scan path perpendicular to the membrane plane,” in Methods in Molecular Biology, 1076, (635–51), 2014. doi:10.1007/978-1-62703-649-8_29.  PDF