AFM analysis, from raw scan to surface metrics
Atlas covers the full AFM workflow: calibrated import, recorded leveling, roughness, terrace and step-height measurement, island segmentation and coverage, line profiles, and PeakForce QNM nanomechanics, all from the same file, checking each channel’s calibration along the way.
What Atlas does with AFM data
Every analysis runs as a documented Block with recorded parameters, so the same result can be reproduced, reviewed, and compared across samples.
Parsing preserves the measurement
.spm files keep their Z calibration, scan size, direction, rate, and channel list. Heights are never leveled, offset, or rescaled at import.
Level once, analyze many times
Plane and line correction is an explicit transform, saved with its model and justification, so every downstream measurement uses the same surface and the original stays reviewable.
Roughness that admits what it hides
Sa, Sq, and Sz come with third and fourth moments that flag sparse raised features, and extremes are traced back to the particle or pit that caused them.
Populations, not a single flake
Height-level segmentation counts islands and reports coverage, area distributions, per-level roughness, and step height against an expected monolayer value.
Line profiles with validity accounting
Profiles are sampled in physical units across the leveled surface, and leave gaps where there is no valid data instead of inventing heights.
Mechanics with a crosstalk check
PeakForce QNM channels become adhesion, dissipation, modulus, and deformation maps, each correlated against height so topographic crosstalk is caught instead of trusted.
Atlas compared with legacy AFM software
Most labs already own capable AFM software. This is where Atlas adds to it, and where your existing tools are still the better choice.
| Capability | Matter42 AtlasCloud or private deployment | Instrument vendor softwaree.g. NanoScope Analysis, XEI | Desktop analysis toolse.g. Gwyddion, MountainsSPIP |
|---|---|---|---|
| Leveling and line correction | Supported. Saved as an explicit transform with the model recorded. | Supported. Flatten and plane-fit tools. | Supported. Extensive leveling options. |
| Roughness parameters | Supported. Sa, Sq, Sz, skew, and kurtosis, with extremes traced to features. | Supported. Standard. | Supported. Standard. |
| Island and terrace segmentation with step heights | Supported. Counts, coverage, area distributions, and step height. | Supported. Particle and grain analysis. | Supported. Grain analysis. |
| Power spectral density and fractal metrics | Not supported. Not yet. | Partly supported. In some packages. | Supported. Standard. |
| Force–distance curve fitting | Not supported. Not yet. | Supported. Standard for supported modes. | Partly supported. In some tools. |
| Nanomechanical maps with crosstalk checks | Supported. Each calibrated channel correlated with height. | Supported. Native property maps; crosstalk checks by eye. | Partly supported. Channel display; analysis by hand. |
| Linking AFM to Raman or PL of the same sample | Supported. Same project, same sample record, correlated analysis. | Not supported. Not offered. | Not supported. Manual. |
| File formats | Partly supported. .spm, calibrated TIFF, and CSV/TSV. | Supported. Own formats. | Supported. Dozens of vendor formats. |
| Results tied to samples and process history | Supported. Leveled surfaces, roughness, and segmentation results are stored as structured outputs linked to the file, parameters, sample, and process run. | Partly supported. Project files on the workstation; sample context kept separately. | Partly supported. Saved project files; sample context kept by hand. |
| Instrument control and acquisition | Not supported. Not an acquisition tool. Keep your instrument software for this. | Supported. Core purpose. | Not supported. Not offered. |
- Supported
- Partly supported
- Not supported
Reflects typical, publicly documented workflows in each category as of September 2026. Capabilities vary by product, version, and add-on module. Product names are trademarks of their respective owners.
Where Atlas stops
A result is only useful if you know its limits. These are the current boundaries, stated in the product the same way.
- Power spectral density, correlation lengths, fractal metrics, and force–distance curve fitting are not offered yet. Keep your current software for them.
- There is no dedicated grain-boundary segmentation yet, and flake shape is not quantified, so “triangular” is still your judgment.
- Atlas will not infer a modulus from an ordinary tapping-mode height image or treat an uncalibrated channel as quantitative.
- It reports calibrated values as the instrument stored them; spotting a badly configured acquisition is left to you, with the correlation checks as evidence.
Files Atlas reads
- Bruker .spm, including PeakForce QNM channels
- Single-channel calibrated TIFF height rasters
- Long-form or matrix CSV and TSV
Questions
- Is Atlas a Gwyddion alternative?
- It covers different ground. Gwyddion remains excellent for broad file-format support and spectral and fractal analysis. Atlas adds recorded, reusable leveling, island statistics tied to each sample, nanomechanics with crosstalk checks, and links to the Raman and PL data from the same sample.
- Which AFM files can I upload?
- Bruker .spm files are parsed natively with their calibration and channel metadata. Other instruments can export a calibrated single-channel TIFF or a CSV/TSV height grid with physical units.
- Does Atlas analyze PeakForce QNM data?
- Yes. Adhesion, dissipation, modulus, and deformation channels are read from the .spm file, and each is correlated with height so you can tell mechanical contrast from topographic crosstalk. Channels without a usable calibration are skipped with a warning.
Bring your AFM data
Send us a file from your own instrument. We’ll run it through Atlas and walk you through every number and caveat it reports.