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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, and the filter buttons (All / Images / Spectra) narrow the grid. 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.

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.

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.

Working with Feature Finder

Open Measurements → Feature finder... to detect point-like features — atoms, molecules, defects, moiré sites — on the current image.

  1. Choose the Detection mode: Maxima for protrusions, Minima for depressions.
  2. Choose a Threshold mode (Above, Below, or Between) and a height threshold so that only genuine features qualify.
  3. Set the Detection settings: Min distance enforces one detection per feature, and Pre-smooth σ suppresses pixel noise before the search.
  4. Click Update preview — detected features are marked on the image and counted.

From the Export section you can write the coordinates to CSV, render a synthetic feature image (a disk at every detection, useful for pair correlation and lattice statistics), or send that feature image straight to the FFT viewer. When Particle Statistics is available, Send to Particle Statistics saves the current detections as a calibrated session feature set for single-image or pooled spatial statistics.

For segmentation-based workflows — particle size statistics, template matching, classification, lattice extraction — use the Feature Counting window (button in the Browse sidebar). It requires the optional features extra:

pip install "probeflow[features]"

For particle spatial-statistics workflows, these detected features and point ROIs can be analysed from Measurements → Features → Particle Statistics.... Use Analyze scan points for real ProbeFlow data, Learn with tutorial for a guided walkthrough, or Model simulations to explore synthetic patterns and null-model behaviour freely before applying the tool to a scan. Particle Statistics is the newest and least user-tested part of ProbeFlow — treat its verdicts as exploratory and verify important results independently. See the Particle Statistics guide and the developer-facing AdStat integration contract.

Beyond the basics

  • ROIs — draw rectangles, ellipses, and lines 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.