T1: Bead analysis (CLI)
Introduction
Microgel beads are transparent, homogeneous, and spherical objects that are ideal test objects for quantitative phase imaging. The DryMass command dm_analyze_sphere can estimate the average refractive index of such homogeneous objects. This is a short tutorial that will reproduce the data presented in supplementary figure 2a of reference [SCG+17].
Prerequisites
For this tutorial, you need:
Python 3.6 or above and DryMass version 0.6.0 or above (see Installing DryMass)
Fiji or Windows Photo Viewer (for data visualization)
Experimental dataset: QLSR_PAA_beads.zip [MSGG19]
Execute dm_analyze_sphere
DryMass comes with a Command-line interface (CLI)
which is made available after the installation.
We will use the DryMass command dm_analyze_sphere
to extract the refractive index values of a population of microgel
beads. Using the command shell of your operating system, navigate
to the location of
QLSR_PAA_beads.zip
and execute the command dm_analyze_sphere
with
QLSR_PAA_beads.zip
as an argument. You will be prompted for
the refractive index of the surrounding medium (1.335), the
detector pixel size in microns (0.14), and the wavelength in
nanometers (647). Simply type in these values (press the Enter
key to let DryMass acknowledge each input). On Windows, this
will look similar to this:
DryMass has created a directory called QLSR_PAA_beads.zip_dm
(the
input argument with _dm appended) which contains the following
files
drymass.cfg: DryMass Configuration file
roi_data.h5: regions of interest (ROIs)
roi_data.tif: phase and amplitude data of the ROIs as a tif file
roi_slices.txt: positions of the ROIs
sensor_data.h5: full sensor QPI data
sensor_data.tif: full sensor phase and amplitude data as a tif file
sensor_roi_images.tif: plotted full sensor phase images with ROIs
sphere_edge_projection_data.h5: simulated (projection) phase and amplitude data
sphere_edge_projection_images.tif: visualization of the sphere analysis of the ROIs as a tif file
sphere_edge_projection_statistics.txt: sphere analysis results as a text file
Examine the results
Let’s have a look at sensor_roi_images.tif (using Fiji or Windows Photo Viewer). This is the first image stored in the tif file:
It shows the full sensor phase image of the first bead. The white rectangle indicates the ROI that was found by DryMass, labeled with the identifier a8dca:1.1. The file sensor_roi_images.tif allows you to check that DryMass has correctly found the objects that you are interested in. If the beads were not detected correctly, we would probably have to adjust the size parameter in the Configuration file (see also dm_extract_roi).
It appears that DryMass has correctly found all beads with the default settings. Next, open the file sphere_edge_projection_images.tif. The identifier of the first ROI is shown at the top, the first column contains phase and intensity of the experimental data, the second column contains the modeled data (with refractive index and radius used for the simulation), and the third column shows the phase-difference as well as line plots through the phase images.
Note that the modeled intensity image is all-one, because the projection model only models the optical thickness and thus only affects the phase data. Also, note that the phase-difference image between data and model only has small deviations in the background phase. If the background phase was not flat, we would have to modify the background correction.
Post-processing
A closer examination of the phase-difference images shows that there seem to be either deformed beads or imaging artifacts in the images with the identifiers (prepend a8dca:): 4.1, 7.1, 24.1, 26.1, 27.1, 35.1, 36.1, 39.1, 40.1, 51.1, 52.1, 55.1, 58.1, 60.1, 64.1, 67.1, and 71.1. Due to their asymmetry we ignore these images in our analysis by editing the configuration file:
[roi]
ignore data = 4.1, 7.1, 24.1, 26.1, 27.1, 35.1, 36.1, 39.1, 40.1, 51.1, 52.1, 55.1, 58.1, 60.1, 64.1, 67.1, 71.1
After executing dm_analyze_sphere
again, we can load the statistics file
sphere_edge_projection_statistics.txt into a statistical analysis application
and compute the average and the standard deviation of the refractive index.
In Python, this can be done with
import numpy as np
ri = np.loadtxt("sphere_edge_projection_statistics.txt", usecols=(1,))
print("average: ", np.average(ri))
print("standard deviation: ", np.std(ri))
which will yield a refractive index of 1.357 ± 0.004 which agrees well with the value given in reference [SCG+17] (1.356 ± 0.004); The small difference can be explained by a slightly modified analysis pipeline and originally more strict selection criteria.