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ProbeFlow GUI

Launch the graphical interface with:

probeflow gui

This guide walks through the most common workflows: loading images, subtracting a background, exploring the FFT, and finding features. The screenshots are generated from the real widgets by scripts/generate_gui_screenshots.py — rerun it after UI changes to refresh them.

Loading images

Use File → Open folder... (or the Open folder button in the sidebar) and pick any folder containing scans. ProbeFlow indexes the folder and shows a thumbnail for every supported file — Createc .dat, Nanonis .sxm, RHK .sm4, plus .VERT and Nanonis spectroscopy files.

Browse mode with a folder of scans loaded

Each card shows the scan size, setpoint, and channel info. The sidebar controls the thumbnail colormap, channel, row alignment, and size; the filter buttons (All / Images / Spectra) narrow the grid, cards can be sorted by name or scan size, and the Bias picker lists the bias values present in the folder so one setpoint can be shown alone. Double-click a thumbnail to open it in the image viewer.

The image viewer showing a terraced surface

The viewer opens on the raw topography with a histogram and contrast controls in the right-hand sidebar (View tab). The toolbar above the image switches channel and colormap; ← Prev / Next → at the bottom steps through the other scans in the folder. Every tool in the viewer is also reachable from the Search box (or Ctrl+K) — type a few letters of what you want ("background", "profile", "fft") and pick the command.

Raw microscope files are treated as read-only: everything below operates on an in-memory copy, and saving always writes a new file.

Subtracting a background

Scans usually come with a tilted plane or scan-line artifacts. Two tools remove them:

  • Processing → Plane/background subtraction... (Ctrl+Shift+B) — polynomial plane fits.
  • Processing → STM scan-line background... (Ctrl+Alt+B) — per-line background estimation designed for terraced STM topographs.

STM scan-line background dialog with a linear fit previewed

In the STM background dialog:

  1. Pick the Fit region — the whole image, or the active ROI if you have drawn one around a flat terrace.
  2. Pick the Line statistic (median is robust to steps and tip changes) and the Background model. Models range from Linear through 2nd/3rd order polynomial, Low-pass and Line by line to the Piezo creep family — switch between them with the dropdown and compare the fits.
  3. Click Preview corrected image. The right-hand plots show the per-line statistic with the fitted background and the residual per scan line, plus residual RMS — switch models until the residuals stop shrinking.
  4. Click Apply. The subtraction is recorded in the processing history (undo with Ctrl+Z), and exports carry the full provenance.

Cleaning up defects

Three everyday repairs, all recorded (and undoable) processing steps:

  • Median filter (despeckle) — Process tab → Smooth → Median. Removes salt-and-pepper noise and single-pixel tip glitches without blurring step edges (unlike Gaussian smoothing).
  • Remove spots — mark a tip change, dirt speck, or glitch with an area ROI (right-click → Remove spots) or a mask from Advanced Edge Detection (Masks section → Remove spots). The region is replaced by a smooth surface interpolated from its surroundings.
  • Crop — draw a rectangle selection (or right-click an area ROI → Crop image to this region), then Image → Transform → Crop to selection. The scale bar, FFT axes, ROIs, and masks all follow the new extent; pixel size is unchanged.

Performing an FFT

Open Measurements → FFT viewer... (Ctrl+Shift+F, or the FFT button in the quick toolbar). The viewer computes the FFT of the current processed image — subtract the background first, or the spectrum is dominated by the surface tilt.

The left pane shows the real-space source with its pixel and q-space resolution; the main pane shows log-magnitude FFT with reciprocal-space axes. The tabs below cover the common reciprocal-space tasks:

  • Inspect — intensity histogram with min/max/brightness/contrast sliders, and a radial profile of the spectrum.
  • Grid — fit a reciprocal lattice to the Bragg peaks.
  • Correction — preview lattice undistortion from the fitted grid.
  • Mains — detect and suppress mains-frequency pickup streaks.
  • Inverse FFT — mask regions of the spectrum and reconstruct the filtered image.
  • Symmetrize — enforce an n-fold (optionally mirrored) symmetry by averaging the image with its rotated copies. Rotated copies are registered back onto the original automatically, so the symmetry axis need not sit at the image centre. Always check the Residual preview: it holds everything symmetrization removed — noise, but also real defects and domain boundaries.

Focus FFT and the zoom buttons home in on the spectral content near the origin, and the Export menu saves the spectrum or filtered image. For a quick periodicity measurement without the full viewer, use Measurements → Find spacing from line profile... on a line ROI.

Detecting features and point-pattern measurements

Under Measurements → Features you can locate point-like features — atoms, molecules, defects, moiré sites — and analyse their spatial pattern:

  • Feature maxima detects local protrusions (or, with an area ROI selected, only within that region), marking them as points in physical (nm) coordinates.
  • Pair correlation computes the pair-correlation function g(r) from the detected points or from point ROIs, reporting the density, the nearest-neighbour median spacing, and the first-peak position. With a calibrated area ROI, g(r) is density-normalised.
  • Point mask / FFT builds a mask from detected features and inspects its FFT.

SIFT-based lattice-vector extraction is an optional tool that needs the lattice extra:

pip install "probeflow[lattice]"

Beyond the basics

  • ROIs — draw rectangles, ellipses, polygons, freehand outlines, lines, and points from the ROI tab; ROIs restrict background fits, FFTs, and statistics, and are saved as sidecar files next to the scan.
  • Measurements — distance and angle measurements, line profiles, ROI statistics, step heights, pair correlation.
  • Spectroscopy — .VERT and Nanonis spectroscopy files open in a dedicated spectrum viewer; positions can be overlaid on the topograph.
  • Export — PNG/PDF/CSV/.sxm/.gwy export with the full processing history embedded, so any image can be reproduced from the raw file.

See cli.md for the command-line equivalents of these workflows.