# Configuration file¶

The DryMass configuration file drymass.cfg is located in the root of the output folder (“_dm” appended to the data path). The configuration file is divided into sections.

## [bg] Background correction¶

DryMass uses the Python library qpimage for background correction. For detailed information on the algorithms (and the corresponding keyword arguments) used, please see qpimage.bg_estimate.

## [holo] Hologram analysis¶

These parameters tune the analysis of off-axis hologram data (if applicable). The parameters shown are passed to qpimage.holo.get_field().

## [meta] Image meta data¶

This section contains meta data of the experiment.

## [output] Supplementary data output¶

This section defines what additional data are written to disk.

## [roi] Extraction of regions of interest¶

The extraction of ROIs is done in drymass.extractroi.extract_roi().

## [specimen] Specimen parameters¶

Prior information about the analyzed object(s).

• size um = 10 (float) – Approximate diameter of the specimen [µm]
This is used as the initial value for the sphere analysis.

## [sphere] Sphere-based image analysis¶

Retrieval of refractive index and radius is done with the Python module qpsphere. The parameters either apply to qpsphere.edgefit.contour_canny() or to qpsphere.imagefit.alg.match_phase(), depending on which analysis approach is used.

• edge coarse = 0.4 (float) – Coarse edge detection filter size
• edge fine = 0.1 (float) – Fine edge detection filter size
• edge clip radius min = 0.9 (float) – Interior edge point filtering radius
• edge clip radius max = 1.1 (float) – Exterior edge point filtering radius
• edge iter = 20 (int) – Maximum number iterations for coarse edge detection
• image fit range position = 0.05 (float) – Fit interpolation range for radius
• image fit range radius = 0.05 (float) – Fit interpolation range for radius
• image fit range refractive index = 0.1 (float) – Fit interpolation range for refractive index
• image fix phase offset = True (fbool) – Fix the simulation background phase to zero
• image iter = 100 (int) – Maximum number of iterations for image fitting
• image stop delta position = 1 (float) – Stopping criterion for position
• image stop delta radius = 0.001 (float) – Stopping criterion for radius
• image stop delta refractive index = 0.0005 (float) – Stopping criterion for refractive index
• image verbosity = 1 (int) – Verbosity level of image fitting algorithm
• method = edge (lcstr) – Method for determining sphere parameters
Valid values are ‘edge’ (edge-detection approach) or ‘image’ (2D phase image fitting).
• model = projection (lcstr) – Physical sphere model
Valid values are defined in qpsphere.models.available. If method=edge, then model must be set to projection. If method=image, setting model to rytov-sc has the best trade-off between accuracy and speed.
• refraction increment = 0.18 (float) – Refraction increment [mL/g]
• radial inclusion factor = 1.2 (float) – Radial inclusion factor for dry mass computation