Igor Pro source package for STM/STS, FFT/QPI, lattice analysis, and modeling workflows

See details from GitHub:

https://github.com/LKong92/Kong_Panel 

𝐊𝐎𝐍𝐆 𝐏𝐚𝐧𝐞𝐥 (KP) is an Igor Pro source package for scanning tunneling microscopy (STM/STS) data processing, interactive visualization, spectral analysis, FFT/QPI workflows, lattice/strain analysis, and simple model simulation. It was developed by Lingyuan Kong as a working research panel: the goal is to keep the everyday analysis path inside one Igor environment, from loading raw Nanonis data to plotting maps, extracting spectra, fitting linecuts, running simulations, and formatting final figures.

Documentation

Start with these two guides when browsing the package on GitHub:

• Panel Guide: visual map of the main panel, each button/control, the action procedure it calls, and the related internal panels.
• Function Index: workflow-organized index of the Function, Proc, Window, Macro, and Menudefinitions parsed from src/*.ipf.
• Startup State: exact list of color-table, physical-constant, graph/color, popup, and compatibility globals recreated when the panel starts in a clean Igor experiment.
• Ready-to-use PXP template: self-contained Igor experiment template with the KP procedure pages and startup objects already packed in.

The repository also includes interactive HTML manuals with search and navigation. After GitHub Pages is enabled for this repository, these links open the rendered manuals directly in a browser:

• Interactive documentation site
• Function Book HTML
• Panel Guide HTML
• Startup State HTML
• Package Summary HTML

GitHub shows the Markdown files directly in the repository browser. The GitHub Pages links above are the preferred way to use the interactive HTML versions from the web.

Selected KP modules and related standalone tools have also been posted separately on WaveMetrics:

• Author page: https://www.wavemetrics.com/user/lykong
• Related standalone posts include the interactive 2D/3D wave displayers, Haldane model, Qi-Wu-Zhang model, Qi-Hughes-Zhang model, multi-order simulator, and twisted honeycomb lattice simulator.

Development Background

KP has been developed as a personal research workflow since 2016-04-15, with the surviving update log beginning on 2021-09-17. The package grew gradually from everyday STM/STS, ARPES, FFT/Fourier-transform analysis, lattice-analysis, and modeling needs rather than from a single one-time software design pass. Parts of the early code base grew from a general ARPES Igor template written by Pierre Richard and Hong Ding.

Demonstration and Citation

Many STM/STS workflows for real-space image analysis, Fourier-transform analysis, and spectroscopic-map processing in KP were developed while processing data for Kong et al., "Cooper-pair density modulation state in an iron-based superconductor," Nature 640, 55-61 (2025). This GitHub package provides the Igor analysis source code used for data analysis in that Nature work; the source data themselves are published with the article. Together, the paper and its associated source data provide a scientific demonstration of the type of real-space STM analysis that can be realized with 𝐊𝐎𝐍𝐆 𝐏𝐚𝐧𝐞𝐥.

If KP is useful for your work, citation of that Nature paper is appreciated:

Kong, L. et al. Cooper-pair density modulation state in an iron-based superconductor.
Nature 640, 55-61 (2025). https://doi.org/10.1038/s41586-025-08703-x

Release Status

• Version prepared for GitHub: 9.04.16, dated 2026-05-18.
• Recommended Igor Pro version: Igor Pro 9 series; this package was prepared from the Igor 9.04 KP line.
• KP-local Nanonis loading code is now in src/KP_NanonisLoaders.ipf.
• Custom color-table waves are loaded from src/KP_NewColorTables.itx when the panel opens.
• Startup globals saved as Igor experiment objects in template.pxp are recreated from src/KP_GlobalState.ipf when the panel opens.
• src/Kong_Igor_panel.ipf is self-contained: opening that panel source also includes all of the action-procedure files used by its controls.
• A clean self-contained Igor experiment template is included at templates/KongPanel_Template_20260520.pxp.

Quick Start

𝐊𝐎𝐍𝐆 𝐏𝐚𝐧𝐞𝐥 can be used in two ways:

• Source install: copy src/ into Igor's User Procedures area, include Load_KongPanel.ipf, and compile. This keeps KP available from any new Igor experiment.
• PXP template: copy templates/KongPanel_Template_20260520.pxp into a dataset folder and open that copy directly. This starts from a self-contained Igor experiment with the KP procedure pages, custom color tables, physical constants, startup globals, and main panel template already packed in.

For the source install, the loader file, src/Load_KongPanel.ipf, includes the main panel recreation file, which then includes the analysis, display, fitting, simulation, and utility procedure files used by the panel. When the procedures compile, Igor adds a Kong Panel menu item; opening the panel loads the 47 custom color-table waves from KP_NewColorTables.itx into root:Packages:NewColortable and recreates the required startup globals documented in docs/STARTUP_STATE.md.

Prerequisite: Install Igor Pro 9

KP is prepared and tested with the Igor Pro 9 series. Install Igor Pro 9 from WaveMetrics before using this package:

• Current and earlier Igor installers: WaveMetrics current software versions
• Igor Pro 9 download and activation notes: WaveMetrics Igor Pro 9 downloads
• Pricing and license options: WaveMetrics Igor Pro pricing

Igor Pro is commercial software. WaveMetrics provides a fully functional 30-day evaluation period; after that, an unlicensed installation enters limited-functionality mode. WaveMetrics offers Standard, Academic, Student, and multi-user/coursework license options. As checked on 2026-05-19, WaveMetrics lists Igor Pro 10 as Windows-only, while Igor Pro 9 provides macOS and Windows installers; KP is tested here against Igor Pro 9.

Installation: User Procedures Method

This is the recommended setup if you want KP available from any clean Igor experiment.

#include "Load_KongPanel"

1. Copy the entire src/ folder into Igor Pro's User Procedures folder. Keeping the files together in a folder named KongPanel is recommended.
   • On macOS this is typically under Documents/WaveMetrics/Igor Pro 9 User Files/User Procedures/.
   • In Igor, use Help -> Show Igor Pro User Files to locate the correct user-files folder.
2. Keep KP_NewColorTables.itx with the .ipf files, preferably inside the same KongPanel or srcfolder. This file contains the 47 custom color-table waves used by KP.
3. Open Igor Pro 9 with a clean experiment.
4. Open the built-in procedure window via Windows -> Procedure Windows -> Procedure Window, or create a new procedure window via Windows -> New -> Procedure.
5. Add this include line at the far left edge of the procedure window:

#include "Load_KongPanel"

6. Compile procedures by clicking Compile in the procedure window, or by using Igor's procedure compile command.
7. Open the panel from Kong Panel -> Open Kong Panel, or run:

Kong_Igor_panel()

You can also explicitly open the loader file using File -> Open File -> Procedure... and select src/Load_KongPanel.ipf. Igor's official documentation recommends #include for shared procedure packages; quoted includes search the Igor Pro User Files User Procedures folder and its subfolders.

Alternative: Per-Experiment PXP Template

If you prefer each dataset to live in its own self-contained Igor experiment, use the included clean template:

templates/KongPanel_Template_20260520.pxp

Recommended workflow:

1. Create a new folder for the dataset you want to analyze.
2. Copy templates/KongPanel_Template_20260520.pxp into that folder.
3. Rename the copied file for the dataset or sample if desired.
4. Open the copied .pxp in Igor Pro 9 and load/analyze the data there.

The template has a short cleaned command history, opens without requiring the source files to be in User Procedures, and contains the adopted KP procedure pages plus the required startup objects. This mode is convenient for keeping each experiment folder portable and independent.

To rebuild your own template from the source package:

1. Start from a clean Igor Pro 9 experiment.
2. Load and compile KP using the User Procedures method above, or explicitly open the KP procedure files from the local src/ folder.
3. Run Kong_Igor_panel() once so the panel opens and the 47 color-table waves are loaded.
4. In Igor's command line, run:

AdoptFiles/A

5. Save the experiment as something like KongPanel_Template.pxp.
6. For a new experiment, create a fresh data folder, copy KongPanel_Template.pxp into that folder, open it, and load/analyze the data there. This keeps each project as an independent .pxp and does not require the daily analysis session to find KP files in User Procedures.

Avoid loading this source package on top of another KP experiment that already contains KP procedure pages with the same function names. A mixed session with duplicate KP procedure pages can produce duplicate-definition errors.

When preparing a GitHub release or ZIP archive, include both src/KP_ColorTables.ipf and src/KP_NewColorTables.itx. Without the .itx file, the source package can still compile, but popups and graph-formatting functions that reference root:Packages:NewColortable:* will not have the custom color waves available.

What 𝐊𝐎𝐍𝐆 𝐏𝐚𝐧𝐞𝐥 Does

KP is broad by design. The panel is arranged as a collection of compact work areas rather than a single linear wizard. The following map summarizes the main functional groups visible in the panel and the corresponding IPF modules.

Nanonis, STM, and STS Data Loading

KP provides loaders and converters for common Nanonis-style STM/STS workflows:

• Auto-load Nanonis .3ds linecuts and grid maps.
• Auto-load .sxm and .nsp topography files.
• Convert grid spectra into 2D maps, 2D linecuts, and 1D spectra.
• Reorder 2D grid linecuts and slice 3D data into 1D/2D outputs.
• Build gate maps and grid maps from automatically loaded Nanonis folders.
• Generate Z maps, R maps, rho maps, and L maps from symmetric energy data.
• Extract topography after loading .sxm/.nsp files.

The KP-local Nanonis loader in KP_NanonisLoaders.ipf supports the panel's .3ds, .sxm, and .nspworkflows. It was rewritten from the small subset of Kohsaka Macro (KM) loading behavior that KP used; KM was written by Yuhki Kohsaka. No full KM package management or unrelated KM UI behavior is included.

Main files:

• src/KP_NanonisLoaders.ipf
• src/UNISOKU3dscutextract.ipf
• src/Miscellaneous_Codes.ipf

Smart Display and Figure Formatting

KP includes fast display tools for 1D, 2D, and 3D waves:

• Interactive 2D wave displayer with color-table selection, normal/inverse color modes, auto range, sigma-style color scaling, graph capture, and quick recoloring.
• Interactive 3D wave viewer for slicing, plotting, and inspecting 3D datasets.
• Waterfall plots, linecut display, voltage maps, ratio maps, and multi-trace copy/cleanup utilities.
• Z-color plotting, trace offsets, line thickness control, active-trace operations, and vector-field plotting.
• Quick formatting buttons for dI/dV, distance-vs-voltage, conductance unit labels, topography maps, axis arrows, plan/auto/rectangle figure styles, and label-on/label-off figure modes.
• RGB image conversion helpers, graph/table cleanup, and graph transfer utilities.

Some of these display tools are also available as standalone WaveMetrics posts on the author page.

Main files:

• src/SmartDisplay.ipf
• src/Smart_3D_Viewer_New.ipf
• src/transfergraph.ipf
• src/Miscellaneous_Codes.ipf

FFT, QPI, Lock-In, Drift, and Symmetrization

The FFT and QPI area is one of the largest parts of KP:

• 2D FFT for real-space STM images, including interpolation, padding, selected-region FFT, and real/complex conversion.
• 1D FFT along linecuts and linecut-filter workflows.
• FFT filtering, low-pass filtering, fixed-width Fourier filtering, and filter-width controls.
• Q-vector extraction with Get A/Get B/Get Q style marker workflows.
• Moving-window phase extraction and phase-difference mapping.
• 2D lock-in plus Fourier-filter workflows.
• Lawler-Fujita drift correction for 2D and 3D data.
• Nanoscale strain-tensor calculation from displacement fields.
• C4, D4, mirror, diagonal, off-diagonal, x, and y symmetrization utilities.
• Phase-referenced QPI and QPI range estimation.

Main files:

• src/FFT.ipf
• src/Lawler-Fujita Drift Correction.ipf
• src/Map_the_phase_difference_between_two_image.ipf
• src/Symmetrization.ipf
• src/PR_QPI.ipf
• src/Shear Correction for C4.ipf

Matrix, Cube, and General Data Operations

KP contains many Igor wave operations that are useful when repeatedly cleaning and reshaping STM/ARPES matrices:

• Delete points, crop by energy or momentum limits, extract marquee regions, and cut NaN edges.
• Interpolate 2D data to arbitrary size, interpolate only along y, and handle uneven y-axis data.
• Rotate, reflect, shear, pad, smooth, normalize, rescale, and coarse-grain matrices.
• Convert complex waves to real/magnitude outputs.
• Convert 3D cubes to linecuts, 2D slices, or summed maps.
• Duplicate, rename, partially select, rescale, smooth, area-normalize, second-differentiate, and sum batches of waves.
• File-to-wave and wave-to-file helper routines.

Main files:

• src/MatrixCalculation.ipf
• src/FFT.ipf
• src/Miscellaneous_Codes.ipf
• src/Procedure.ipf

Spectroscopy, Gap Maps, and Tip-Height Experiments

KP includes STS analysis routines used for maps, linecuts, and individual spectra:

• 1D and 2D gap extraction.
• Gaussian and GCB-style gap-map workflows.
• Multi-peak 1D linecut fitting.
• 2D Gaussian peak finding and 1D multi-peak extraction.
• BCS/Dynes and SC-SC fitting utilities.
• Load and average individual STS spectra.
• Normalize spectra and linecuts using fitted backgrounds, numerical references, and waterfall-style traces.
• Convert I/V to dI/dV by differentiation.
• Apply voltage-divider corrections to single spectra, regular linecuts, and randomly sampled linecuts.
• Format one wave according to another wave/template.

Main files:

• src/MultipeakforLinecut.ipf
• src/General_Simu.ipf
• src/Miscellaneous_Codes.ipf
• src/UNISOKU3dscutextract.ipf

ARPES and Template Utilities

KP still carries a large ARPES/template section inherited from earlier Igor workflows:

• Load common ARPES text formats and plot EDC/MDC-style data.
• Build matrix and 3D matrix views from ARPES cuts.
• Convert angle to momentum and handle kx-ky, kz, and photon-energy maps.
• Rescale momentum, normalize map data, combine energy/momentum ranges, and build Fermi-surface images.
• Add Fermi-level markers, symmetrize EDC matrices, divide by Fermi functions, and keep positive/negative branches.
• Remove backgrounds, build equivalent waves, and handle Scienta/A1-style inputs.

Main file:

• src/Pierre's Template.ipf

Lattice, Strain, Segregation, and Moire Tools

KP includes tools for real-space lattice work and moire analysis:

• Draw and append honeycomb, triangular, and square lattice overlays on topography.
• Fit lattice overlays using lattice constant, rotation, and offsets.
• Simulate honeycomb and triangular-lattice images.
• Calculate twisted bilayer/trilayer graphene lattice patterns.
• Estimate twist-angle maps and moire wavelengths.
• Perform lattice-segregation analysis.
• Calculate RDF/length statistics and cursor-based point information.
• Apply shear correction and C4 shear workflows.

Main files:

• src/Triangle Lattice_Graphene_like.ipf
• src/Lattice Segregation.ipf
• src/General_Simu.ipf
• src/Shear Correction for C4.ipf

Model Simulation

KP contains model simulators and teaching/research calculations that can be launched from the panel:

• Haldane model, including A(k, omega) and Berry-curvature style outputs.
• Qi-Wu-Zhang model.
• Qi-Hughes-Zhang superconducting QAH/topological superconductor model, including slab, LDOS, and A(k, omega, L) utilities.
• FeSC tight-binding, FeSC k.p, QPI, LDOS, and Fermi-surface simulations.
• Majorana bound-state splitting, CdGM states, Landau-level DOS, vortex-line and superconducting vortex simulations.
• PDW, CDW, multi-order, vortex-pair, topological-defect, and 2D PDM simulations.
• Temperature convolution, batch temperature convolution, RCSJ model, and P(E) theory calculations.
• Global SI constants for command-line and modeling work: q0, h, G0, muB, kB, eV, meV, and m0.
• Source-install startup restoration for root-level template globals used by older graph/color/popup workflows, including topgraph*, colorsetedc*, colorinverseedc, zn_cons, and related strings. The exact defaults and validation commands are listed in docs/STARTUP_STATE.md.
• Matrix-Hamiltonian construction with complex/text Pauli matrices (s0/sx/sy/sz, st0/stx/sty/stz), tensor products (mpc/mpn/mpt), text matrix addition (plust), and automated Pauli-sequence builders (automatrixT/automatrixC).
• Band calculations and model-Hamiltonian demonstrations.

Main files:

• src/Models.ipf
• src/ModelingTunneling.ipf
• src/General_Simu.ipf

Documentation

The docs/ folder contains both release notes and generated code references.

• docs/CHANGELOG.md: polished GitHub-facing changelog.
• docs/STARTUP_STATE.md: startup-state compatibility note listing the globals restored from template.pxp.
• docs/KP_update_log_20260518.md: short update entry for the 2026-05-18 GitHub preparation.
• docs/KP_update_log_original.rtf: original update-log copy.
• docs/KP_update_log_raw.txt: plain-text conversion of the original log.
• docs/code_inventory.md: source extraction, include layout, and Nanonis loader notes.
• docs/FUNCTION_BOOK.html: color-coded function manual generated from all IPF files.
• docs/FUNCTION_INDEX.md: GitHub-readable Markdown function index, organized by workflow rather than by IPF file.
• docs/assets/kong_panel_main.png: GitHub-friendly main-panel image.
• docs/PANEL_GUIDE.html: main-panel image plus button-to-procedure guide.
• docs/PANEL_GUIDE.md: Markdown version of the panel guide.
• docs/function_catalog.json: machine-readable function catalog.
• docs/panel_catalog.json: machine-readable panel/control catalog.

Function Book

The generated function manual covers every Function, Proc, Window, Macro, and Menu definition found in src/*.ipf.

Open this file in a browser for the best reading experience:

docs/FUNCTION_BOOK.html

The HTML manual is styled to resemble Igor procedure-code structure: keywords are blue, function/procedure names are visually separated, signatures use a monospace font, and panel callback controls are marked in purple. It is organized by workflow and role, not by IPF file, while still showing source file and line for navigation. The current generated catalog contains 3203 entries from 25 IPF files.

For GitHub browsing, use:

docs/FUNCTION_INDEX.md

For the main 𝐊𝐎𝐍𝐆 𝐏𝐚𝐧𝐞𝐥 layout, button map, and secondary/internal panel overview, use:

docs/PANEL_GUIDE.html

Repository Layout

• src/Load_KongPanel.ipf: recommended loader; compiles all KP sources and adds the Kong Panel menu.
• src/Kong_Igor_panel.ipf: self-contained panel entry; opening it includes all required action-procedure files.
• src/KongPanel.ipf: compatibility umbrella include.
• src/KP_NanonisLoaders.ipf: KP-local Nanonis .3ds, .sxm, and .nsp loader.
• src/*.ipf: KP analysis, display, simulation, fitting, formatting, and panel modules.
• docs/: changelog, update-log copies, code inventory, and function reference.
• scripts/build_function_book.py: regenerates the function book, function index, panel guide, and JSON catalogs.

External Igor Procedure Dependencies

KP uses several standard WaveMetrics/Igor procedure files through Igor's include system:

• Resize Controls
• Peak AutoFind
• Global Fit 2

These files are not vendored into this repository. They should be available from Igor Pro/WaveMetrics procedure libraries or installed separately in the user's Igor procedure path.

Attribution

KP was developed by Lingyuan Kong for STM data analysis and model simulation workflows, with development beginning on 2016-04-15 according to the preserved project log. This GitHub version was prepared with the help of Codex. Earlier parts of the package grew from a general ARPES Igor template by Pierre Richard and Hong Ding, with some signal-enhancement functions referring to Peng Zhang's curvature-analysis macro.

License

𝐊𝐎𝐍𝐆 𝐏𝐚𝐧𝐞𝐥 is released under the MIT License.

Copyright (c) 2026 Lingyuan Kong. See LICENSE for details.