DryMass documentation

DryMass is a user-friendly quantitative phase imaging analysis software. This is the documentation of DryMass version 0.6.1.

Contents:

• Introduction
  • What is DryMass?
  • What are typical use cases of DryMass?
  • What is quantitative phase imaging?
  • How should I cite DryMass?
• Theory Notes
  • Computation of cell dry mass
  • Relative and absolute dry mass
  • Range of validity
    • Dependency on imaging wavelength
    • Dependency on protein concentration
    • Dependency on pH, temperature, and salts
    • Refraction increment and the mass of cells
  • Default parameters in DryMass
• Getting started
  • Installing DryMass
    • Upgrade
    • Known issues
  • Command line interface
    • dm_convert
    • dm_extract_roi
    • dm_analyze_sphere
  • Configuration file
    • [bg] Background correction
    • [holo] Hologram analysis
    • [meta] Image meta data
    • [output] Supplementary data output
    • [roi] Extraction of regions of interest
    • [specimen] Specimen parameters
    • [sphere] Sphere-based image analysis
  • Troubleshooting
    • Freezing / no output
    • None of the above
• Tutorials
  • T1: Bead analysis (CLI)
    • Introduction
    • Prerequisites
    • Execute dm_analyze_sphere
    • Examine the results
    • Post-processing
  • T2: HL60 cell analysis (CLI)
    • Introduction
    • Prerequisites
    • Find regions of interest
    • Set 2nd order polynomial background correction
    • Perform sphere analysis
    • Plot the results
    • Discussion
  • T3: Correcting for background and geometry (CLI)
    • Introduction
    • Prerequisites
    • Take a glimpse at the data
    • Select 2nd order polynomial background correction
    • Include beads that are close to each other
    • Include beads at the border of the sensor image
    • Exact determination of radius and refractive index
• Code examples
  • Dry mass computation with radial inclusion factor
  • Comparison of relative and absolute dry mass
• Code reference
  • Command-line interface
    • cli.config
    • cli.definitions
    • cli.dialog
    • cli.parse_funcs
    • cli.plot
  • Data analysis
    • anasphere
    • converter
    • extractroi
  • Helper classes and methods
    • search
    • util
    • roi
• Changelog
  • version 0.6.1
  • version 0.6.0
  • version 0.5.0
  • version 0.4.1:
  • version 0.4.0
  • version 0.3.3
  • version 0.3.2
  • version 0.3.1
  • version 0.3.0
  • version 0.2.0
  • version 0.1.4
  • version 0.1.3
  • version 0.1.2
  • version 0.1.1
  • version 0.1.0
• Bilbliography

Indices and tables

• Index
• Module Index
• Search Page