{"id":131,"date":"2017-08-08T20:12:51","date_gmt":"2017-08-08T20:12:51","guid":{"rendered":"https:\/\/home.physics.wisc.edu\/gilbert2\/?page_id=131"},"modified":"2026-03-09T02:30:05","modified_gmt":"2026-03-09T02:30:05","slug":"software","status":"publish","type":"page","link":"https:\/\/home.physics.wisc.edu\/gilbert\/software\/","title":{"rendered":"Software"},"content":{"rendered":"

Software<\/h1>

GG Macros<\/h2>\r\n

The Gilbert Group Macros (GG Macros) were developed by Benjamin Gilbert (bgilbert@lbl.gov<\/a>) and Pupa Gilbert (pupa@physics.wisc.edu<\/a>). The GG Macros run on Mac and PC, are ready-to-use, free of charge, and are recommended to analyze synchrotron spectromicroscopy data, that is, images stacked as a function of photon energy, or polarization of the illuminating x-rays.<\/p>\r\n

1. Download Igor Pro 8 or 9 from http:\/\/www.wavemetrics.com\/ <\/a>\r\n2. Download the GG Macros and their Manual from GitHub: https:\/\/github.com\/b0gilbert\/GG-macros.<\/a>\r\n3. Follow the instructions in the manual to place the macros in the correct folders on your computer.\r\n4. Contact Pupa Gilbert at pupa@physics.wisc.edu<\/a> if you have any questions.\r\n5. If our GG Macros contribute to your work, please consider citing them using their Zenodo DOI: https:\/\/doi.org\/10.5281\/zenodo.17314121<\/a>.<\/p>\r\nIn a nutshell, the GG macros enable you to:\r\n\r\nDo quantitative analysis of the orientation of carbonate crystals. For example, the aragonite (CaCO3<\/sub>) tablets in nacre can be distinguished by their crystal orientation as shown below. At a single linear polarization (left) two tablets (magenta dots, or blue dots) may display very similar gray levels, but their orientation can be quite distinct, when fully analyzed at multiple polarizations (see J4 in the manual).<\/b>\r\n\r\n\"\"<\/a>\r\n\r\nObtain the 3D crystallographic orientation of carbonate crystals or apatite crystals using either PELICAN or PIC mapping. The in-plane orientation of the c-axis (termed c’ angle) is displayed as hue, and the out-of-plane orientation is displayed as brightness, from full color to black in PIC maps.<\/b>\r\n\r\n\"\"<\/a>\r\n\r\nExtract spectra from mouse-drawn ROIs<\/b>\r\n\r\n\"\"<\/a>\r\n\r\nExtract spectra from a single pixel<\/b>\r\n\r\n\"\"<\/a>\r\n\r\nExtract spectra from pixels along a line<\/b>\r\n\r\n\"\"<\/a>\r\n\r\nDo peak fitting of extracted spectra<\/b>\r\n\r\n\"\"<\/a>\r\n\r\nDisplay the spatial distribution of individual components with known spectra<\/b>\r\n\r\n\"\"<\/a>\r\n\r\nThe individual components and their relative concentrations can then be combined in a quantitative \u201cComponent Map\u201d if there are 1, 2, or 3 component in the system analyzed, or Myriad Map (MM) if there are more than 3 components. See J4 or J5 in the Manual for component maps or MMs.<\/strong>\r\n\r\n\"\"<\/a>\r\n\r\nYou can calculate Polarization-Enabled Large Input of Crystal Angles at the Nanoscale (PELICAN) maps. <\/strong>See K in the Manual for PELICAN mapping.<\/strong>\r\n\r\n\"You<\/a>\r\n\r\nYou can extract histograms of misorientations from every pair of adjacent pixels in the PELICAN map. Making sure that the pixel size is well-matched to the nanocrystal size provides the most significant information.<\/strong>\r\n\r\n\"You<\/a><\/div><\/div><\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"

The Gilbert Group Macros (GG Macros) were developed by Benjamin Gilbert (bgilbert@lbl.gov) with extensive interaction and feedback from Pupa Gilbert. The GG Macros run on Mac and PC, are ready-to-use, free of charge, and are recommended to analyze synchrotron spectromicroscopy data, that is, images stacked as a function of photon energy, or polarization of the…<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"_uw_migration_status":"in-progress","_uw_gutenberg_post_content_before_migration":"","footnotes":""},"class_list":["post-131","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/home.physics.wisc.edu\/gilbert\/wp-json\/wp\/v2\/pages\/131","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/home.physics.wisc.edu\/gilbert\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/home.physics.wisc.edu\/gilbert\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/home.physics.wisc.edu\/gilbert\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/home.physics.wisc.edu\/gilbert\/wp-json\/wp\/v2\/comments?post=131"}],"version-history":[{"count":31,"href":"https:\/\/home.physics.wisc.edu\/gilbert\/wp-json\/wp\/v2\/pages\/131\/revisions"}],"predecessor-version":[{"id":1201,"href":"https:\/\/home.physics.wisc.edu\/gilbert\/wp-json\/wp\/v2\/pages\/131\/revisions\/1201"}],"wp:attachment":[{"href":"https:\/\/home.physics.wisc.edu\/gilbert\/wp-json\/wp\/v2\/media?parent=131"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}