{"id":1015,"date":"2026-02-15T15:01:59","date_gmt":"2026-02-15T15:01:59","guid":{"rendered":"https:\/\/mtyaron.com\/microscopy\/?page_id=1015"},"modified":"2026-05-04T12:52:16","modified_gmt":"2026-05-04T12:52:16","slug":"4dstem-mega-navigator","status":"publish","type":"page","link":"https:\/\/mtyaron.com\/microscopy\/4dstem-mega-navigator\/","title":{"rendered":"4DSTEM Mega Navigator"},"content":{"rendered":"<p align=\"center\"><span style=\"font-size: xx-large; font-weight: bold\">4DSTEM Mega Navigator<\/span><br \/><span style=\"font-size: large; font-weight: bold\">(A freeware 4D navigator for 4D-STEM data analysis)<\/span><\/p>\n<p><img decoding=\"async\" loading=\"lazy\" data-id=\"1034\"  src=\"https:\/\/mtyaron.com\/microscopy\/wp-content\/uploads\/sites\/2\/2026\/02\/icon-for-4DSTEM.png\" alt=\"\" width=\"100\" height=\"100\" class=\"aligncenter size-thumbnail wp-image-1034\" \/><\/p>\n<p align=\"center\"><font size=\"2\">last update: 04-May-2026<\/font><\/p>\n<p align=\"center\" display=\"inline\">Ver. 0.1.4 Download link :  <a href=\"https:\/\/tinyurl.com\/4k5rsxcy\" target=\"_blank\" rel=\"noopener noreferrer\"><img decoding=\"async\" alt=\"\" src=\"https:\/\/mtyaron.com\/microscopy\/wp-content\/uploads\/sites\/2\/2020\/02\/Very-Basic-Download-icon-e1387481864919-1.png\" \/><\/a><\/p>\n<p align=\"center\" display=\"inline\">Manual : <a href=\"https:\/\/mtyaron.com\/microscopy\/wp-content\/uploads\/sites\/2\/2026\/03\/Manual-4DSTEM-Mega-Navigator-Ver.-0.1.0.pdf\" target=\"_blank\" rel=\"noopener noreferrer\"><img decoding=\"async\" alt=\"\" src=\"https:\/\/mtyaron.com\/microscopy\/wp-content\/uploads\/sites\/2\/2020\/02\/Very-Basic-Download-icon-e1387481864919-1.png\" \/><\/a><\/p>\n<p><a href=\"https:\/\/mtyaron.com\/microscopy\/wp-content\/uploads\/sites\/2\/2026\/05\/MegaNAV-GUI.png\"><img decoding=\"async\" data-id=\"1082\"  src=\"https:\/\/mtyaron.com\/microscopy\/wp-content\/uploads\/sites\/2\/2026\/05\/MegaNAV-GUI.png\" alt=\"\" width=\"1000\" class=\"aligncenter size-full wp-image-1082\" \/><\/a><br \/>\n<\/p>\n<p><u><span style=\"font-size: large; font-weight: bold\">Highlights<\/span> (<b style='color:red;'>new features are marked in red<\/b>)<\/u>:<\/p>\n<ul>\n<li><strong>No installation required (portable) &#8211; just unzip the file (download link above) and double click the run.bat file.<\/strong><\/li>\n<li>Supported formats:<br \/>\n<div class=\"su-list\" style=\"margin-left:0px\">\n<ul>\n<li><i class=\"sui sui-check\" style=\"color:#333\"><\/i> Zarr (.zarr folder)<\/li>\n<li><i class=\"sui sui-check\" style=\"color:#333\"><\/i> NumPy Compressed (.npz)<\/li>\n<li><i class=\"sui sui-check\" style=\"color:#333\"><\/i> NumPy Array (.npy)<\/li>\n<li><i class=\"sui sui-check\" style=\"color:#333\"><\/i> NanoMEGAS Blockfile (.blo)<\/li>\n<li><i class=\"sui sui-check\" style=\"color:#333\"><\/i> Dectris Arina (.h5)<\/li>\n<\/ul>\n<\/div><\/li>\n<li>File conversion:<br \/>\n<div class=\"su-list\" style=\"margin-left:0px\">\n<ul>\n<li><i class=\"sui sui-check\" style=\"color:#333\"><\/i> Merlin MIB (.mib) files to Zarr folder<\/li>\n<li><i class=\"sui sui-check\" style=\"color:#333\"><\/i> TFS Velox MRC files (.mrc+.xml) to Zarr folder<\/li>\n<\/ul>\n<\/div><\/li>\n<li>Build virtual apertures: BF, ADF, HAADF, Bragg &#038; Bragg grid.<\/li>\n<li>Strain (\u00b5Probe) mapping analysis. REMARK: Not fully tested &#8211; use with care !!!<\/li>\n<li>COM &#038; DPC\/iDPC analysis. REMARK: Not fully tested &#8211; use with care !!!<\/li>\n<li>Manual Navigator (nm\/px) and DP (nm<sup>-1<\/sup>\/px) calibration.<\/li>\n<li>Semi-automatic central-beam (CB) alignment.<\/li>\n<li>Zoom to region of interest (ROI).<\/li>\n<li>Change the color maps (cmap) of the Navigator and the DP.<\/li>\n<li>Includes two folders with examples of 4DSTEM datasets (synthetic &#038; real data).<\/li>\n<li>Sub-pixel movement of the detectors and the bragg discs.<\/li>\n<li>Scalebars added for calibrated Navigator and Diffraction.<\/li>\n<li>File saving with and without overlays.<\/li>\n<li>New tab for selecting and cropping the large dataset + saving the reduced dataset as Zarr or NPZ.<\/li>\n<li>In the Filters tab added the option to create intensity profiles in the NAV and DP + option to calibrate the pixel size.<\/li>\n<li><b style='color:red;'>Added the option of editing the dataset Metadata and save it with the pixels calibration to .zattrs file<\/b>.<\/li>\n<li><b style='color:red;'>Zoom in\/out of the NAV and the DP with mouse wheel. Right click menu to reset zoom<\/b>.<\/li>\n<li><b style='color:red;'>Save DP\/NAV stores also the axes lables and colorbars<\/b>.<\/li>\n<li><b style='color:red;'>New tab &#8220;DP Distortion&#8221; (still under development) &#8211; compensate for detector and beam alignment distortions (important for BraggGrid and Strain analysis)<\/b>.<\/li>\n<li><b style='color:red;'>In &#8220;Crop\/Rotate ROI&#8221; tab &#8211; added te option to export the full dataset to Zarr ot NPZ<\/b>.<\/li>\n<\/ul>\n<p><span style=\"font-size: large; font-weight: bold\"><u>Future Features<\/u>:<\/span><\/p>\n<ul>\n<li>Support for more file formats and file conversions.<\/li>\n<p>and more &#8230;\n<\/ul>\n<\/p>\n<p><\/br><\/p>\n<hr>\n<hr>\n<p><u><span style=\"font-size: large; font-weight: bold\">Software Libraries Used in 4D-STEM Mega Navigator<\/span><\/u>:<\/p>\n<p>The following external libraries were used in the development of the 4D-STEM Mega Navigator.<\/p>\n<p><strong><u>Core Scientific Libraries<\/u>:<\/strong><\/p>\n<ul>\n<li><strong>NumPy<\/strong> &#8211; Harris, C. R. et al. (2020). Array programming with NumPy. Nature, 585, 357\u2013362. <a href=\"https:\/\/doi.org\/10.1038\/s41586-020-2649-2\" rel=\"noopener\" target=\"_blank\">https:\/\/doi.org\/10.1038\/s41586-020-2649-2<\/a><\/li>\n<li><strong>SciPy<\/strong> &#8211; Virtanen, P. et al. (2020). SciPy 1.0: Fundamental algorithms for scientific computing in Python. Nature Methods, 17, 261\u2013272. <a href=\"https:\/\/doi.org\/10.1038\/s41592-019-0686-2\" rel=\"noopener\" target=\"_blank\">https:\/\/doi.org\/10.1038\/s41592-019-0686-2<\/a><\/li>\n<li><strong>Matplotlib<\/strong> &#8211; Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science &#038; Engineering, 9(3), 90\u201395. <a href=\"https:\/\/doi.org\/10.1109\/MCSE.2007.55\" rel=\"noopener\" target=\"_blank\">https:\/\/doi.org\/10.1109\/MCSE.2007.55<\/a><\/li>\n<\/ul>\n<p><strong><u>Large-Scale Data Processing and 4D-STEM Libraries<\/u>:<\/strong><\/p>\n<ul>\n<li><strong>LiberTEM<\/strong> &#8211; 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. <a href=\"https:\/\/doi.org\/10.21105\/joss.02006\" rel=\"noopener\" target=\"_blank\">https:\/\/doi.org\/10.21105\/joss.02006<\/a><\/li>\n<li><strong>Dask<\/strong> &#8211; Rocklin, M. (2015). Dask: Parallel computation with blocked algorithms and task scheduling. Proceedings of the 4th Python in Science Conference. <a href=\"https:\/\/doi.org\/10.25080\/Majora-7b98e3ed-013\" rel=\"noopener\" target=\"_blank\">https:\/\/doi.org\/10.25080\/Majora-7b98e3ed-013<\/a><\/li>\n<li><strong>Zarr<\/strong> &#8211; Zarr Developers. Zarr: An implementation of chunked, compressed, N-dimensional arrays for Python. Software available at <a href=\"https:\/\/zarr.dev\" rel=\"noopener\" target=\"_blank\">https:\/\/zarr.dev<\/a><\/li>\n<li><strong>Numcodecs (Blosc compression)<\/strong> &#8211; numcodecs Developers. numcodecs: A Python package providing buffer compression and transformation codecs. Available at <a href=\"https:\/\/numcodecs.readthedocs.io\" rel=\"noopener\" target=\"_blank\">https:\/\/numcodecs.readthedocs.io<\/a><\/li>\n<li><strong>Quantem<\/strong> &#8211; quantem Developers. quantem: Electron microscopy data handling tools for Python. Available at <a href=\"https:\/\/github.com\/electronmicroscopy\/quantem\" rel=\"noopener\" target=\"_blank\">https:\/\/github.com\/electronmicroscopy\/quantem<\/a><\/li>\n<\/ul>\n<p><strong><u>Graphical User Interface Framework<\/u>:<\/strong><\/p>\n<ul>\n<li><strong>Qt for Python (PySide6)<\/strong> &#8211; Qt Company. Qt for Python (PySide6) Documentation. Available at <a href=\"https:\/\/doc.qt.io\/qtforpython-6\/\" rel=\"noopener\" target=\"_blank\">https:\/\/doc.qt.io\/qtforpython-6\/<\/a><\/li>\n<\/ul>\n<hr>\n<hr>\n","protected":false},"excerpt":{"rendered":"<p>4DSTEM Mega Navigator(A freeware 4D navigator for 4D-STEM data analysis) last update: 04-May-2026 Ver. 0.1.4 Download link : Manual : Highlights (new features are marked in red): No installation required (portable) &#8211; just unzip the file (download link above) and double click the run.bat file. Supported formats: File conversion: Build\u2026<\/p>\n<p class=\"continue-reading-button\"> <a class=\"continue-reading-link\" href=\"https:\/\/mtyaron.com\/microscopy\/4dstem-mega-navigator\/\">Continue reading<i class=\"crycon-right-dir\"><\/i><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"folder":[],"_links":{"self":[{"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/pages\/1015"}],"collection":[{"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/comments?post=1015"}],"version-history":[{"count":114,"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/pages\/1015\/revisions"}],"predecessor-version":[{"id":1160,"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/pages\/1015\/revisions\/1160"}],"wp:attachment":[{"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/media?parent=1015"}],"wp:term":[{"taxonomy":"folder","embeddable":true,"href":"https:\/\/mtyaron.com\/microscopy\/wp-json\/wp\/v2\/folder?post=1015"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}