Show3DSlices

Show3DSlices lays slices of a volume side by side across an axis, with a synced crosshair, so you can read out depth structure at a glance instead of scrubbing one slice at a time.

Tip

Run this exact notebook with the Colab badge above, or View or download this notebook on GitHub. For finished results, use HTML and file export to export interactive HTML or share a trusted notebook with widget state.

Show synthetic data generation code

Hide synthetic data generation code

import numpy as np

# Synthetic ptychographic-object-phase volume: atom columns that drift across
# depth, so scrubbing through z shows the lattice shift slice by slice.
depth, size = 24, 256
row, col = np.mgrid[0:size, 0:size]
spacing = 20
sites = np.arange(spacing // 2, size, spacing)
volume = np.zeros((depth, size, size), dtype=np.float32)
for z in range(depth):
    shift = 6.0 * np.sin(2 * np.pi * z / depth)  # columns sway with depth
    for r0 in sites:
        for c0 in sites:
            volume[z] += np.exp(-(((row - r0 - shift) ** 2 + (col - c0) ** 2)) / (2 * 2.5 ** 2))
volume.shape, volume.dtype

((24, 256, 256), dtype('float32'))

Slices across depth

Pass the stack with depth and lateral calibration so Show3DSlices can draw calibrated scale bars. The crosshair links the panels; move it on one to see the same position on all.

from quantem.widget import Show3DSlices

Show3DSlices(
    volume,
    sampling=(0.3, 0.18, 0.18),
    units=("nm", "nm", "nm"),
    title="Synthetic object phase",
)