The words of this tutorial, step by step. The text lives in src/smappy/tutorial/topics/; the directions it follows are in src/smappy/tutorial/STYLE.md.
1. card: Rendering in 2D and 3D
What is drawn, how SMAPpy draws it, what to change for a figure, how to save it, and the 3D view.
spoken: This tutorial is about the picture: how it is drawn, how to change it, and the 3D view.
2. card: A picture of positions
A localization is a position with an uncertainty. Rendering draws each one as a small blur, or counts them per pixel.
What the picture looks like is a choice; the table underneath stays the same.
spoken: A localization is a position with an uncertainty. Rendering draws each one as a blur, or counts them per pixel.
3. Each layer draws only what passes its filter. A quick button in bold has a bound: a new table starts with a few, on precision and fit quality.
4. Any column can be filtered: the list below the buttons has them all, and each layer keeps its own bounds.
5. Grouped, each blink is one localization: its positions averaged and its photons added, so it is more precise.
6. Ungrouped, every frame of every blink is drawn: more localizations, each one less precise.
7. Link settings, beside grouped, sets how far a molecule may move between frames, and how many dark frames a blink may have.
8. The filter and the grouping also decide what the analysis plugins measure: what is drawn is what is measured.
9. Render precision draws each localization as wide as it is uncertain: well-localized ones are sharp, poor ones are soft.
10. Hist counts the localizations in each pixel. Nothing is smoothed, so up close the picture is grainy, but it hides nothing.
11. Gauss draws every localization with the same width, set under more.
12. Contrast sets how many of the brightest pixels are saturated. A smaller value saturates more, and faint structure comes up.
13. The colour table, LUT, maps brightness to colour.
14. White background turns the picture over for a figure: ink on paper, with the colours kept.
15. Save keeps a PNG as you see it, or renders a TIFF at a pixel size you choose: in colour, or as intensities to measure.
16. The picture's axes need not be x and y. With z as the second axis, the same table is a side view of the ring.
17. Any column works: photons against frame, say, to see bleaching. Reset brings back the ordinary picture.
18. View, 3D view opens the same layers in 3D, with their filters and colours.
19. Drag to turn it, scroll to zoom. Top, front and side jump to those views; fit brings the whole box back.
20. Colour by depth shows which parts are near and which are far.
21. The slab is the box that is drawn. Narrowed in z it is a thin section; it can also follow a region drawn in 2D.
22. card: What to remember
- Render mode: precision for the picture, hist to see exactly what is there.
- Contrast, LUT, white background: how it looks, never what it is.
- Save: a PNG as shown, or a TIFF at a chosen pixel size.
- 3D view: the same layers, turned, with a slab.
spoken: That is rendering. Next: plugins, which measure what is drawn.