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: SMAPpy in three minutes
From raw camera frames to a super-resolution picture: fit the frames, check the fit, look at the result.
The acquisition here is simulated, so nothing depends on a microscope.
spoken: In three minutes: from raw camera frames to a super-resolution picture.
2. card: How the picture is made
In each frame only a few molecules shine, far enough apart to be seen one by one.
Fitting each spot finds its centre to a few nanometres. Thousands of frames of positions make the picture.
spoken: A reminder: only a few molecules shine in each frame. Fitting each spot finds its centre, and many frames make the picture.
3. Raw camera frames are fitted in the Localize tab.
4. Each section is a fitter. Gaussian 2D is for ordinary data; the spline fitters use a bead calibration, for 3D.
5. The question mark beside a plugin opens its page. F1 does the same.
6. What the plugin does, how it works, and what each setting means. Help, Plugin documentation, lists every page.
7. Open Gaussian 2D and choose the acquisition. Any file of a Micro-Manager or NDTiff dataset will do.
8. SMAPpy normally reads the camera from the file. This simulated file says nothing about it, so its numbers are typed in here.
9. Preview fits one frame and shows what it found, before anything is saved.
10. Every spot should have its circle. If noise is circled, or a spot is missed, change the cutoff in detection.
11. The cutoff is the one setting that usually needs a look; the rest can stay as they are.
12. Then Run.
13. The picture builds up while the fit runs, so a bad acquisition shows early.
14. When it is done, the localizations are saved beside the acquisition, and the picture is complete.
15. Zoomed in, the ring is sharp far below the size of a camera pixel.
16. The Render tab sets how the picture looks: filters, colours, and grouping of blinks.
17. card: That is all it takes
- Localize fits the frames: choose the file, check the camera, preview, run.
- Render shows the result.
- Analysis measures it.
- The ? beside a plugin explains it.Next: the tour of SMAPpy, with filters, layers and grouping.
spoken: That is all it takes. Next, the tour of SMAPpy: filters, layers and grouping.