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Spectroscopy Browser

The Spectroscopy Browser is a searchable, filterable tree of every spectroscopy trace associated with the current workspace - organized hierarchically as Image -> Site -> Trace, not a flat table.

Spectroscopy workspace context

What it shows

Open the browser from the toolbar. Each top-level entry is a source image; underneath it, spectra are grouped into sites (locations that were measured, possibly repeatedly or as a Z-stack) and finally individual traces.

This is useful when you want to:

  • see at a glance which images have associated spectroscopy, and how much
  • search across image/site/file/channel/position instead of scanning the thumbnail grid
  • open several related traces into the same comparison plot

Search and filters

  • A search box filters the tree live by image name, site, file, channel, or position text.
  • Four checkboxes narrow the tree further: Current image (only spectra tied to the image currently shown in the main preview), Z-stacks, Matrix, and Low confidence (spectra whose automatic image assignment - see Spectroscopy Overview - wasn't confident).

Common actions

Right-click an entry in the tree for:

  • Open - opens the trace in a spectroscopy popup
  • Assign to current image - manually attaches this spectrum to whichever image is currently displayed, overriding the automatic assignment
  • Clear manual assignment - reverts to the automatic assignment

Selecting several entries (Shift/Ctrl-click) and opening them feeds a shared comparison plot instead of opening one popup per trace - see Spectroscopy Overview for the comparison workflow this leads into.

A separate, per-file dialog: Spectro Summary

Right-clicking a thumbnail's spectroscopy miniature (or certain "show spectros for this file" actions) opens a different, per-file dialog - a small modal listing just that file's own spectroscopy entries, with its own preview thumbnail, channel selector, marker-color picker, and (for matrix files) a colormap combo. This is a lighter-weight, single-file complement to the global searchable browser above, not the same window.

Relationship to thumbnail markers

The browser complements the thumbnail-grid workflow rather than replacing it.

Use:

  • the thumbnail grid when you want image-first navigation with spatial context (see Thumbnail Grid for the marker symbols, low-confidence indicator, and stack badges drawn there)
  • the browser when you want to search/filter across everything at once, independent of which image is currently on screen

Plot controls

Once a trace or comparison is open in a spectroscopy popup, it supports a richer set of display controls, including:

  • grid, line, point, and dark-background toggles
  • per-trace styling for colour, thickness, and line style
  • legend editing for position, font size, background, and border
  • smoothing and derivative filters
  • typography and export or copy actions