Tutorials¶
These tutorials build up from simply viewing images to full single-cell analysis. You don't need to read them in order, but each section assumes you're comfortable with the one before it.
A quick note on cell tables¶
UELer works in two modes, and it's worth knowing which one you're in:
- Without a cell table, UELer is an image viewer. You can browse channels, overlay masks and annotations, capture regions of interest, and batch-export images.
- With a cell table loaded, UELer becomes a linked single-cell explorer — scatter plots, histograms, heatmaps, clustering, and the cell gallery all light up and stay synchronized with the image.
This isn't just a suggestion: the viewer only loads the analytical plugins once a cell table is present. With no cell table, the right panel shows just the ROI manager and Batch export plugins. See Working with a Cell Table for how to load one.
Part 1 · Essentials¶
Everything here works on images alone — no cell table required.
| Tutorial | What you'll learn |
|---|---|
| Basic Usage | Launch the viewer, pick an FOV, select channels, and navigate |
| Guided Setup | The dialog that opens on first load, and the key fields that link your table to the images |
| User Interface | A reference map of the four regions and every left-panel control |
| Display Settings | Set the viewer up so it shows your data correctly — pixel size, cache, downsampling, contrast |
| Regions of Interest | Capture, tag, and browse ROIs that persist across sessions |
| Map Mode | Stitch multiple FOVs into one spatial canvas (opt-in feature) |
| Batch Export | Export full FOVs, ROIs, and single-cell crops to image files |
Part 2 · Single-Cell Analysis¶
These features require a cell table (a per-cell feature CSV, e.g. from ark-analysis).
| Tutorial | What you'll learn |
|---|---|
| Working with a Cell Table | Load a table, understand linked selection, and use the cell gallery |
| Scatter & Histogram | Explore marker distributions with linked brushing |
| Clustering & Annotation | Heatmaps, FlowSOM clustering, and saving annotation checkpoints |
New here?
Start with Basic Usage, then skim the User Interface reference. Before you trust what you see — or export it — walk through Display Settings once for the dataset. Then, with a cell table, move on to Working with a Cell Table.