Home 4DSTEM Mega Navigator

4DSTEM Mega Navigator

4DSTEM Mega Navigator
(A freeware 4D navigator for 4D-STEM data analysis)

last update: 20-October-2026

Ver. 0.2.0 Download link :    /    Example Datasets :

4DSTEM Mega Navigator Tutorials – YOUTUBE Channel

Manual :


Highlights (new features are marked in red):

  • No installation required (portable) – just unzip the file (download link above) and double click the run.bat file.
  • Supported formats:
    • Zarr (.zarr folder)
    • NumPy Compressed (.npz)
    • NumPy Array (.npy)
    • NanoMEGAS Blockfile (.blo)
    • Dectris Arina (.h5)
    • Native py4DSTEM HDF5 (.h5)
    • Gatan DM3/DM4 (.dm3/.dm4)
  • File conversion:
    • Merlin MIB (.mib) files to Zarr folder + Batch conversion
    • TFS Velox MRC files (.mrc+.xml) to Zarr folder + Batch conversion
  • Clustering and Phase Identification: (under contruction and evaluation process !!!)
    • New Clustering tab using PCA and K-means for unsupervised segmentation.
    • Automatic selection of the number of clusters (Auto-K).
    • Clustering based on diffraction intensities or Bragg-peak distributions.
    • Cluster-average diffraction patterns and crystallographic comparison between clusters.
    • New Phase / Orientation tab for CIF-based phase identification and crystal orientation mapping using simulated diffraction templates.
    • Ground-truth validation for synthetic datasets.
  • Advanced µProbe Strain Analysis: (under contruction and evaluation process !!!)
    • Improved µProbe Strain (advanced) workflow, now enabled by default..
    • More robust Bragg-peak detection, subpixel refinement, and outlier rejection.
    • Improved reference lattice construction and quality diagnostics.
    • Advanced strain-map export to NPZ.
  • Build virtual apertures: BF, ADF, HAADF, Bragg & Bragg grid.
  • Better BraggGrid Presentation: g1/g2 arrows appear after definition / optional g1/g2 overlays.
  • Strain (µProbe) mapping analysis. REMARK: Not fully tested – use with care !!!
  • COM & DPC/iDPC analysis. REMARK: Not fully tested – use with care !!!
  • Manual Navigator (nm/px) and DP (nm-1/px) calibration.
  • Semi-automatic central-beam (CB) alignment.
  • Zoom to region of interest (ROI).
  • Change the color maps (cmap) of the Navigator and the DP.
  • Includes two folders with examples of 4DSTEM datasets (synthetic & real data).
  • Sub-pixel movement of the detectors and the bragg discs.
  • Scalebars added for calibrated Navigator and Diffraction.
  • File saving with and without overlays.
  • New tab for selecting and cropping the large dataset + saving the reduced dataset as Zarr or NPZ.
  • In the Filters tab added the option to create intensity profiles in the NAV and DP + option to calibrate the pixel size.
  • Added the option of editing the dataset Metadata and save it with the pixels calibration to .zattrs file.
  • Zoom in/out of the NAV and the DP with mouse wheel. Right click menu to reset zoom.
  • Save DP/NAV stores also the axes lables and colorbars.
  • New tab “DP Distortion” (still under development) – compensate for detector and beam alignment distortions (important for BraggGrid and Strain analysis).
  • In “Crop/Rotate ROI” tab – added te option to export the full dataset to Zarr ot NPZ.
  • Unified file/folder opening dialog and Drag-and-drop support for datasets and Zarr folders.
  • Improved BraggGrid peak detection and lattice fitting.
  • New rotational averaging of diffraction-pattern intensity profiles.
  • Improved BraggGrid peak detection and lattice fitting + Interactive angular-sector selection and visualization.

Future Features:

  • Support for more file formats and file conversions.

    • and more …


Software Libraries Used in 4D-STEM Mega Navigator:

The following external libraries were used in the development of the 4D-STEM Mega Navigator.

Core Scientific Libraries:

Large-Scale Data Processing and 4D-STEM Libraries:

  • LiberTEM – Clausen, A. et al. (2020). LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy. Journal of Open Source Software, 5(50), 2006. https://doi.org/10.21105/joss.02006
  • Dask – Rocklin, M. (2015). Dask: Parallel computation with blocked algorithms and task scheduling. Proceedings of the 4th Python in Science Conference. https://doi.org/10.25080/Majora-7b98e3ed-013
  • Zarr – Zarr Developers. Zarr: An implementation of chunked, compressed, N-dimensional arrays for Python. Software available at https://zarr.dev
  • Numcodecs (Blosc compression) – numcodecs Developers. numcodecs: A Python package providing buffer compression and transformation codecs. Available at https://numcodecs.readthedocs.io
  • Quantem – quantem Developers. quantem: Electron microscopy data handling tools for Python. Available at https://github.com/electronmicroscopy/quantem

Graphical User Interface Framework:

Comments are closed.