{"id":48,"date":"2026-08-23T15:37:07","date_gmt":"2026-08-23T15:37:07","guid":{"rendered":"https:\/\/qoy.vxf.mybluehost.me\/website_11aa7f22\/getting-started\/"},"modified":"2026-09-17T04:59:15","modified_gmt":"2026-09-17T04:59:15","slug":"getting-started","status":"publish","type":"page","link":"https:\/\/aquaphotomics.com\/software\/aquagrammar\/getting-started\/","title":{"rendered":"Getting started"},"content":{"rendered":"\r\n<p class=\"wp-block-paragraph\">Your first Aquagram\u00ae, in four steps. Nothing here needs configuring, and you do not need to supply a file: two datasets come bundled.<\/p>\r\n\r\n\r\n<a id=\"install\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"before-you-begin\">Before you begin<\/h2>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">&#8211;<\/p>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li>Windows 10 or Windows 11.<\/li>\r\n\r\n\r\n<li>No instrument required. Preview reads prepared files only; it never connects to a MicroNIR.<\/li>\r\n\r\n<\/ul>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">The four steps are always listed down the left side of the window, and the current one is highlighted. You can click back to an earlier step at any time without losing your work.<\/p>\r\n\r\n\r\n<a id=\"open-a-file\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"step-1-%c2%b7-open-a-file\">Step 1 \u00b7 Open a file<\/h2>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">You are offered three cards.<\/p>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li><strong>Open your own file<\/strong> \u2014 drag a MicroNIR file onto the dashed card, or select <strong>Choose file<\/strong>. Accepted: <code>.sam<\/code>, vendor CSV, vendor XLSX.<\/li>\r\n\r\n\r\n<li><strong>Demo 1 \u2014 Natural Systems<\/strong> \u2014 select <strong>Open Demo 1<\/strong> for nine bundled groups of rock and mineral scans.<\/li>\r\n\r\n\r\n<li><strong>Demo 2 \u2014 Water<\/strong> \u2014 select <strong>Open Demo 2<\/strong> for four bundled groups of water-source scans.<\/li>\r\n\r\n<\/ul>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">If you are here to learn the tool, start with Demo 1. AquaGrammar moves to step 2 by itself once the file is read.<\/p>\r\n\r\n\r\n<a id=\"select-groups\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"step-2-%c2%b7-select-sample-groups\">Step 2 \u00b7 Select sample groups<\/h2>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Your file is split into sample groups, each showing its name and how many repeat scans it contains \u2014 <code>Stone1 (n=15)<\/code> means fifteen repeats of Stone1.<\/p>\r\n\r\n\r\n<ol class=\"wp-block-list\">\r\n<li><strong>Tick the groups you want.<\/strong> Nothing is selected initially. Unticked groups are excluded completely \u2014 they contribute to nothing later. <strong>Select all<\/strong> and <strong>Clear selection<\/strong> are in the bottom-right corner.<\/li>\r\n\r\n\r\n<li><strong>Check the counter<\/strong> above the list (&quot;4 of 9 selected&quot;). It always reflects your current choice.<\/li>\r\n\r\n\r\n<li><strong>Choose an SNV range.<\/strong> Three options sit below the list:<\/li>\r\n\r\n<\/ol>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li><strong>1st overtone 1300\u20131600<\/strong> \u2014 the recommended choice. This is the region the twelve Classic-12 coordinates actually fall in, so each spectrum is normalized against the range being plotted.<\/li>\r\n\r\n\r\n<li><strong>Full range<\/strong> \u2014 normalizes across every wavelength in the file.<\/li>\r\n\r\n\r\n<li><strong>Combination 1100\u20131300<\/strong> \u2014 normalizes on the combination band.<\/li>\r\n\r\n<\/ul>\r\n\r\n\r\n<ol class=\"wp-block-list\">\r\n<li>Select <strong>Continue to row processing<\/strong>.<\/li>\r\n\r\n<\/ol>\r\n\r\n\r\n<p class=\"wp-block-paragraph\"><strong>Sort<\/strong> and the <strong>Cards \/ List<\/strong> toggle only change how groups are displayed. They never change your selection.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">What happens when you continue: SNV is applied to every selected scan over the range you chose, each wavelength is then standardized across every scan in the file as <code>(value \u2212 mean) \/ SD<\/code>, and finally repeats are averaged within each group. This is automatic and has no other settings.<\/p>\r\n\r\n\r\n<a id=\"process-rows\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"step-3-%c2%b7-process-rows\">Step 3 \u00b7 Process rows<\/h2>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">The left panel, <strong>Inputs for Aquagram\u00ae<\/strong>, lists one row per group you selected, under the heading *Original groups \u00b7 SNV applied*. Each row has a coloured dot showing the colour its line will take.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">You can go straight on \u2014 just tick the rows you want to plot and skip to step 4. Or combine them first, using the <strong>Operation<\/strong> panel on the right:<\/p>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li><strong>Average<\/strong> \u2014 the mean of two or more ticked groups.<\/li>\r\n\r\n\r\n<li><strong>Add<\/strong> \u2014 the sum of two or more ticked groups.<\/li>\r\n\r\n\r\n<li><strong>Subtract<\/strong> \u2014 adjusts any number of ticked groups against one baseline group you choose separately, producing one result per adjusted group.<\/li>\r\n\r\n<\/ul>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Select <strong>Create average row<\/strong> (or sum\/subtract) and the result appears under *Processed results* on the left. You can rename it with the pencil icon, remove it with the \u00d7, or feed it back into another operation.<\/p>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">When the rows you want are ticked, select <strong>Generate Classic-12 Aquagram\u00ae<\/strong>.<\/p>\r\n\r\n\r\n<a id=\"result\"><\/a>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"step-4-%c2%b7-read-and-export\">Step 4 \u00b7 Read and export<\/h2>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">Every row you ticked becomes one coloured line, listed in the legend beneath the chart.<\/p>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li><strong>Select a legend entry<\/strong> to hide or show that line.<\/li>\r\n\r\n\r\n<li><strong>Zoom<\/strong> with \u2212 \/ + above the chart; above 100% you can drag to pan.<\/li>\r\n\r\n\r\n<li><strong>Hover a line<\/strong> to read its WAMACS label, wavelength, and value.<\/li>\r\n\r\n\r\n<li><strong>View overall mean table<\/strong> opens the fixed twelve-row table \u2014 the mean across the rows you plotted.<\/li>\r\n\r\n\r\n<li><strong>Export XLSX \/ CSV \/ PNG \/ JPG.<\/strong> XLSX and CSV give you one column per plotted line, enough to rebuild the chart elsewhere. PNG and JPG capture the chart together with its legend.<\/li>\r\n\r\n<\/ul>\r\n\r\n\r\n<p class=\"wp-block-paragraph\">To begin again, click an earlier step in the left rail, or open a different file.<\/p>\r\n\r\n\r\n<h2 class=\"wp-block-heading\" id=\"next\">Next<\/h2>\r\n\r\n\r\n<ul class=\"wp-block-list\">\r\n<li>Want to be walked through it properly? \u2192 <a href=\"\/software\/aquagrammar\/tutorial\/\">Tutorial<\/a><\/li>\r\n\r\n\r\n<li>Want to know what SNV and standardization actually do? \u2192 <a href=\"\/software\/aquagrammar\/user-guide\/\">How AquaGrammar works<\/a><\/li>\r\n\r\n\r\n<li>Something went wrong? \u2192 <a href=\"\/software\/aquagrammar\/troubleshooting\/\">Troubleshooting<\/a><\/li>\r\n\r\n<\/ul>\r\n","protected":false},"excerpt":{"rendered":"<p>Your first Aquagram\u00ae, in four steps. Nothing here needs configuring, and you do not need to supply a file: two datasets come bundled. Before you begin &#8211; The four steps are always listed down the left side of the window, and the current one is highlighted. You can click back to an earlier step at [&hellip;]<\/p>\n","protected":false},"author":0,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"nf_dc_page":"","om_disable_all_campaigns":false,"_monsterinsights_skip_tracking":false,"footnotes":""},"class_list":["post-48","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Getting started - AquaGrammar<\/title>\n<meta name=\"description\" content=\"Make your first Aquagram in four steps using the bundled sample data. 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