Glossary & FAQ

Words

Absorbance — how strongly a sample takes up light at each wavelength. The measurement AquaGrammar works from.

Aquagram® — the radar chart AquaGrammar produces: one closed line per plotted row, drawn around the twelve Classic-12 coordinates. A visual summary of a configured analysis, not a diagnosis and not a substitute for the underlying spectrum.

Aquaphotomics — the study of light–matter interactions, especially water-related spectral patterns, used to help describe the state of a system. It needs appropriate experimental design and interpretation.

Baseline — in a Subtract operation, the single row every other selected row is measured against. Each adjusted row produces its own result.

Classic-12 — the twelve WAMACS coordinates AquaGrammar plots, found experimentally in the water first overtone and lying between 1342 and 1512 nm. Preview uses this set and does not let you change it.

Combination band — the water absorption near 1190 nm, combining the first overtone of the O-H stretch with the O-H bend. Weaker than the first overtone, which makes it useful for thick or strongly absorbing samples. One of the three SNV ranges.

First overtone — the water absorption region around 1300–1600 nm, where all twelve Classic-12 coordinates sit. AquaGrammar labels its default SNV range 1300–1600 nm and takes in every measured point between 1298 and 1601 nm.

NIR spectrum — measured values arranged against wavelength in the near-infrared. The input evidence; an Aquagram® is a summary derived from it.

Perturbation — a defined change, or a comparison of defined conditions, used to study how a spectrum responds. Preview reads prepared files; it does not create a perturbation or control an instrument.

Preprocessing — a documented transformation applied before analysis. Preview applies a fixed sequence (SNV, standardization, repeat averaging). You cannot adjust it by hand; the only choice offered is the SNV range.

Processed row — a row you built with Average, Add, or Subtract. It sits alongside the original groups and can be plotted, renamed, deleted, or used as an input to another operation.

Provenance — the record of where a result came from: source file, selected groups, workflow version, SNV range, and the formula behind each row. Shown above the chart and written into exports.

Reflectance — the proportion of incident light returned by a sample. Related to absorbance but not interchangeable with it.

Repeat — one of several scans of the same sample. Stone1 (n=15) means fifteen repeats. Repeats are averaged within their group.

Sample group — a named set of repeats in your file. Groups are what you select in step 2, and averaging happens within them, never across them.

SNV (Standard Normal Variate) — normalizes one scan against itself by subtracting its mean and dividing by its standard deviation, so scans can be compared by shape rather than overall level.

Standardization — after SNV, each wavelength is put on a common footing across every scan in the file, as (value − mean) / SD.

System state — the condition of a system under study. An Aquagram® can help visualize associated patterns; it does not by itself establish a medical or biological conclusion.

WAMACS — water matrix coordinates: wavelength ranges where particular water-related absorbance bands are found. See Classic-12.

Questions

Who is this help site for? Beginners going from a MicroNIR file to an Aquagram® for the first time. Experienced users may still find How AquaGrammar works useful as a statement of exactly what the fixed workflow does.

What should I practise on? The two bundled datasets — Demo 1 (Natural Systems) and Demo 2 (Water). They are included, always available, and nothing you do to them is permanent.

Can I connect a MicroNIR and scan? No. Preview reads prepared .sam, vendor CSV, and vendor XLSX files. It never connects to or controls an instrument.

Which SNV range should I choose? Start with 1st overtone 1300–1600 nm — it is the default and matches published aquagram practice. Switch to the combination band if your sample is thick or absorbing enough to saturate the detector at the stronger band. See How AquaGrammar works for the reasoning.

My file will not open. What now? Confirm it genuinely is a MicroNIR .sam, vendor CSV, or vendor XLSX covering the Classic-12 range — renaming a different format will not work. Note the exact message and see Troubleshooting.

Does an Aquagram® diagnose anything? No. It visualises spectral coordinates. A chart alone establishes no diagnosis, treatment recommendation, or biological conclusion; the meaning comes from the experiment behind it.

How do I start over? There is no Reset button. Click an earlier step in the left rail to go back without losing anything, or open a different file to replace the session.

Does AquaGrammar save my work? No. Preview keeps no projects and no history. Only the files you export yourself persist after closing.

Why does Windows warn me when I install it? The installer is unsigned, so Microsoft Defender SmartScreen flags it as not-yet-recognised. It is a reputation check, not a virus scan. The Download page shows exactly what to click.

What data does it collect? None. AquaGrammar reads the file you open and writes the exports you ask for. Use anonymised files in public demonstrations, and keep personal names out of sample labels.

Will there be more features? Preview deliberately does one thing. What comes next depends on what people tell us they need — which is the point of releasing a preview. Send thoughts to aquagrammar@aquaphotomics.com.

Where do I report a problem? aquagrammar@aquaphotomics.com. Include what you were doing, the exact message, the file type or bundled demo, and your Windows version.