Command line interface¶
DryMass comes with a command line interface (CLI). To use the CLI, a command shell is required, such as the command prompt Cmd.exe on Windows, or Terminal.app on MacOS. Please note that if DryMass is installed in a virtual environment, then the DryMass CLI is only available if this environment is activated.
This command converts experimental data on disk to the TIF file format for use with Fiji/ImageJ and to the hdf5-based qpimage data file format. The experimental data files are loaded with the qpformat library, which supports several quantitative phase imaging file formats. If a specific format is not supported, please create an issue at the qpformat issue page. A typical use case of dm_convert on Windows is
which is equivalent to
d: cd "data\path\to" dm_convert experiment
If this command is run initially for an experimental data set, the user
is asked to enter or confirm imaging wavelength and detector pixel size.
Then, a new directory
d:\\data\path\to\experiment_dm is created
with the following files:
- the user-editable drymass configuration file which is used in subsequent analysis steps
- the experimental data (including meta data) in the hdf5-based qpimage data file format
- the experimental phase and amplitude series data as a tif file, importable in Fiji/ImageJ
Note that it is possible to edit the drymass.cfg file and to re-run the dm_convert command (or any other of the commands below) with these updated parameters.
This command automatically finds and extracts regions of interest (ROIs) and performs an automated background correction for single-cell analysis. The usage is the same as that of dm_convert:
The command dm_extract_roi automatically runs dm_convert if it has not been run before. If ROI detection fails, the search parameters have to manually be updated in the drymass configuration file. The most important parameter is the diameter of the specimen in microns (“size um” in the specimen section); all other parameters are defined in the roi section. Note that the default parameters for the roi section are not written to the configuration file until dm_extract_roi is run. The following files are created by dm_extract_roi:
- the extracted, background-corrected ROI data (including meta data) in the hdf5-based qpimage data file format
- the extracted, background-corrected ROI data as a tif file, importable in Fiji/ImageJ
- the locations of the ROIs found as a txt file
- rendered sensor phase images with labeled ROIs; only created if “roi images” is set to “True” in the output section of the drymass configuration file
This command is used for the analysis of spherical phase objects such as liquid droplets, beads, or suspended cells. The basic principle is thoroughly described in reference [SSM+16]. In short, this approach assumes that the objects found with dm_extract_roi are homogeneous and spherical which allows to extract parameters such as radius and refractive index from a single phase image (as opposed to tomographic approaches that require an acquisition of multiple phase images from different directions). The parameters for the sphere analysis, such as analysis method and scattering model, are defined in the sphere section of the drymass configuration file. For an overview of the available models, please refer to the qpsphere docs. The following files are created by dm_analyze_sphere (METHOD is the analysis method and MODEL is the scattering model defined in drymass.cfg):
- the quantitative sphere simulation data using MODEL with the parameters obtained with the combination of METHOD and MODEL for each of the ROIs obtained with dm_extract_roi in the hdf5-based qpimage data file format
- rendered phase and intensity images of the input ROIs and the corresponding simulation, a difference, and a line plot through the phase image for visual inspection as a tif file, importable in Fiji/ImageJ
- the analysis results, including refractive index, radius, and relative and absolute dry mass as a text file.