Introduction

The Problem

Quantitative phase imaging (QPI) is a fundamental imaging technique that visualizes the retardation of electromagnetic radiation as it passes through an object. The parameter that governs this retardation is called refractive index. In biological imaging, QPI is an important tool to measure the dry mass or the refractive index (related to mass density [Bar52] [DW52]) of single cells and tissues, which enables a profound characterization of the investigated samples.

Why qpimage?

In the Guck group, we make heavy use of QPI and thus require a reliable and well-documented software library that, independent of the particular QPI setup used, allows us to address QPI-related research questions. Qpimage attempts to unify QPI analysis by providing a unique and user-friendly API for working with QPI data, including the choice of input data (complex field, phase with amplitude or intensity, hologram), memory-efficient and fast storage of large data sets (using HDF5, phase and amplitude data are stored separately), or robust and extendable background correction techniques (ramp fit, binary mask). The main reason for the development of qpimage is our QPI analysis software DryMass.

Citing qpimage

If you are using qpimage in a scientific publication, please cite it with:

(...) using qpimage version X.X.X (available at
https://pypi.python.org/pypi/qpimage).

or in a bibliography

Paul Müller (2017), qpimage version X.X.X: Phase image analysis
[Software]. Available at https://pypi.python.org/pypi/qpimage.

and replace X.X.X with the version of qpimage that you used.

Furthermore, several ideas implemented in qpimage have been described and published in scientific journals:

  • Phase retrieval from holographic images with a gaussian filter is implemented according to [SSM+15].
  • Phase background image correction with a ramp filter fitted to a border of the image data was used in [SSM+15] and [SSM+16].
  • Intensity background correction by dividing by a reference intensity image for tomographic imaging was used in [SCG+17].