a repo for cataloging ideas around integrating spatial mass spec with vitessce

• Support 2D spatial layers.

  • MxIF imaging channel (high resolution; OME-TIFF format)
  • IMS channel (annotated m/z ratio; currently in imzML format or .csv)
  • Segmentation polygons (in-house text format, should standardize)

• Support multiple layers and blending of 2D layers.

• Support a m/z spectrum view. Selection from IMS 2D spatial layer allows user to view entire m/z spectrum for point selection (or aggregate spectrum of multiple points).

• Support spatial selection (through segmentation or manual area selection) and aggregate underlying spectra (e.g. mean spectrum).

• For annotated m/z ratios, provide visual indication of confidence of annotation.

• Provide optional (toggle) view of QC summary for current IMS (data pending).

• Selecting layers (via brush or annotation)

  • If annotated m/z (spase spectrum), fetch 2d slice at single m/z and render.
  • If raw data (dense spectrum), sample a few m/z in range initially and then load rest?
  • NOTE: The visual encoding for this selection should likely be dynamic (ie. spectrum for dense/raw data and table/heatmap/etc for annotated layers).

• Pan-and-zoom of rendered layers

  • Hopefully handled by deck.gl.

• Coordination between separate views

  • Look at current implementation linking 2D-Scatterplots in vitessce.
  • Coordinated pan & zoom between views
  • Look at how higlass defines these linked views (ie. shared zooming but not panning)

• Aggregate 2d spatial annotated m/z channels (ie. biologically meaningful grouping; m/z may be far apart)

  • likely some type of dropdown to select multiple annotated m/z.

• Create aggregate spectrum from 2d selection.