Examples

Examples are complete workflows built from real or simulated datasets. Tutorials explain individual GUI concepts; examples should show the whole path from input data to exported result.

Current examples

Example	Current state	Use it for
Synthetic quickstart	Runnable generator and GUI workflow are included.	Testing installation, screenshots, and first NNLS/NNMF run.
Stitching and preprocessing	Workflow and decision guide are drafted; needs real tiled data.	Demonstrating tile parsing, overlap, scan direction, and preprocessing.
Reproduce Figure 1	Publication planning page; needs final figure assets.	Organizing paper figures and reproducibility files.
CARS/SRS label-free data	Workflow outline; needs representative dataset.	Showing CRS/CARS/SRS decomposition.
SWIR reflection data	Workflow outline; needs representative dataset.	Showing wavelength-axis and fixed-H workflows.
4D fluorescence unmixing	Workflow outline; needs representative 4D stack.	Showing z/time browsing and cross-slice fitting.

What each finished example should include

Item	Why it matters
Input data description	Lets users confirm dimensionality, axis order, and expected component count.
wavelength.json or axis instructions	Prevents silent channel-index analysis when a physical axis is expected.
Preset files	Makes seed setup, colors, solver settings, and histogram levels reproducible.
Step-by-step GUI actions	Makes the example usable without reading the full reference first.
Expected result images and H spectra	Gives users a way to tell whether their run is working.
Exported TIFF/CSV outputs	Documents what should be produced for downstream analysis or Fiji/ImageJ.

Media checklist

When adding screenshots and GIFs, prioritize media that removes ambiguity about where to click:

Priority	Media
1	Synthetic quickstart: load TIFF, import spectra, run fixed-H NNLS, export composite.
2	ROI Manager: add ROI, assign component, rename, change color, plot spectrum.
3	Result viewer: channel browsing, histogram/LUT adjustment, H export, composite export.
4	4D loading: axis-role dialog and result slice browsing.
5	Stitching: tile folder selection, regex helper, preview table, stitch output.