Examples

2D Refocusing of an HL60 cell

The data show a live HL60 cell imaged with quadriwave lateral shearing interferometry (SID4Bio, Phasics S.A., France). The diameter of the cell is about 20µm.

refocus_cell.py

import matplotlib.pylab as plt
import numpy as np
import unwrap

import nrefocus

from example_helper import load_cell

# load initial cell
cell1 = load_cell("HL60_field.zip")

# refocus to two different positions
cell2 = nrefocus.refocus(cell1, 15, 1, 1)  # forward
cell3 = nrefocus.refocus(cell1, -15, 1, 1)  # backward

# amplitude range
vmina = np.min(np.abs(cell1))
vmaxa = np.max(np.abs(cell1))
ampkw = {"cmap": plt.get_cmap("gray"),
         "vmin": vmina,
         "vmax": vmaxa}

# phase range
cell1p = unwrap.unwrap(np.angle(cell1))
cell2p = unwrap.unwrap(np.angle(cell2))
cell3p = unwrap.unwrap(np.angle(cell3))
vminp = np.min(cell1p)
vmaxp = np.max(cell1p)
phakw = {"cmap": plt.get_cmap("coolwarm"),
         "vmin": vminp,
         "vmax": vmaxp}

# plots
fig, axes = plt.subplots(2, 3, figsize=(8, 4.5))
axes = axes.flatten()
for ax in axes:
    ax.xaxis.set_major_locator(plt.NullLocator())
    ax.yaxis.set_major_locator(plt.NullLocator())

# titles
axes[0].set_title("focused backward")
axes[1].set_title("original image")
axes[2].set_title("focused forward")

# data
mapamp = axes[0].imshow(np.abs(cell3), **ampkw)
axes[1].imshow(np.abs(cell1), **ampkw)
axes[2].imshow(np.abs(cell2), **ampkw)
mappha = axes[3].imshow(cell3p, **phakw)
axes[4].imshow(cell1p, **phakw)
axes[5].imshow(cell2p, **phakw)

# colobars
cbkwargs = {"fraction": 0.045}
plt.colorbar(mapamp, ax=axes[0], label="amplitude [a.u.]", **cbkwargs)
plt.colorbar(mapamp, ax=axes[1], label="amplitude [a.u.]", **cbkwargs)
plt.colorbar(mapamp, ax=axes[2], label="amplitude [a.u.]", **cbkwargs)
plt.colorbar(mappha, ax=axes[3], label="phase [rad]", **cbkwargs)
plt.colorbar(mappha, ax=axes[4], label="phase [rad]", **cbkwargs)
plt.colorbar(mappha, ax=axes[5], label="phase [rad]", **cbkwargs)

plt.tight_layout()
plt.show()

Compare available Metrics for Refocusing

The HL60 cell data used is described in refocus_cell.py.

compare_metrics.py

import nrefocus
from nrefocus.metrics import METRICS
import matplotlib.pyplot as plt

from examples.example_helper import load_cell

# load initial cell and create rf object
rf = nrefocus.iface.RefocusNumpy(field=load_cell("HL60_field.zip"),
                                 wavelength=647e-9,
                                 pixel_size=0.139e-6,
                                 kernel="helmholtz")

# autofocus the image for each metric
my_metrics = list(METRICS.keys())

fig, axes = plt.subplots(1, len(my_metrics), figsize=(12, 5))

for i, mt in enumerate(my_metrics):
    af_vals = rf.autofocus(metric=mt,
                           minimizer="lmfit",
                           interval=(-5e-6, 5e-6),
                           ret_field=True,
                           ret_grid=True)
    d, grid, field = af_vals

    axes[i].plot(grid[0], grid[1])
    axes[i].axvline(d, color='k', ls='--')
    axes[i].set_title(f"Metric {mt}")

fig.suptitle("Comparison of Metrics")
fig.tight_layout()
plt.show()