Samples

The microscope images one sample at a time. A sample (in the code: a specimen) is a geometry: where its labelled structures are, as a pure function of the seed and the position, over an endless coverslip. Everything after that does not depend on the sample: the dyes and their photophysics, the light path, the PSF, the camera and the drift (Physics). A labelled structure of a sample is a target. Each target has its own label (a dye in a mode, a labelled %, a DNA-PAINT imager concentration), and only the mounted sample's labels make light.

Sample	What it is	Targets	Pages
Cell field (CellField, the default)	Adherent cells packed on the coverslip: cell outline, cytoplasm height, nucleus, microtubules, nuclear pores	Microtubules (mt-*), nuclear pores (npc-*), imaged together; the nuclear lamina (lamin-*), unlabelled by default	World model, Structures
Nanorulers (Nanorulers)	DNA-origami rods lying on the coverslip, each with three spots of docking strands 80 nm apart; bent in the plane as a worm-like chain	Docking strands (ruler-*)	DNA-origami nanorulers
Bead sample (Beads)	A bare coverslip with only the fiducial beads (single or in clumps)	none: the beads' settings	Fiducial beads
Fluorescent slide (Slide)	A uniform dye layer on the coverslip (5 µm of a TetraSpeck-colour mix at 10 µM by default)	none: its thickness, dye, concentration and bleach half-time	Fluorescent slide

On top of the cell field or the nanorulers, optional fiducial beads (gold, TetraSpeck, FluoSpheres, nanodiamonds) mark the drift: on the coverslip, on the sample or in a gel layer, off by default (Fiducial beads; viewer: Fiducial beads, Micro-Manager: Fiducials, CLI: --fid-*). Changing them is not a new sample: the illumination history stays.

The registry of samples and targets is data/specimens.json: each target's option prefix and core structure id, and (in data/dyes/library.json typicalLabels) its usual dye and labelled % per label mode.

Switching samples

Where	How
Viewer	Specimen select (Sample section). Switching shows that sample's option groups and label, and zooms to a scale that suits it.
Micro-Manager	SampleHolder (a state device: CellField, Nanorulers, Beads, Slide), or the Specimen config group of the shipped configurations. Each sample with settings of its own has its own device for its geometry and label (CellField, Nanorulers, FluorescentSlide); the bead sample's settings are the Fiducials device's.
CLI	--specimen CellField (default), --specimen Nanorulers, --specimen Beads or --specimen Slide (or 0 / 1 / 2 / 3); the nanorulers' options are --origami-* and their label's --ruler-*, the beads' --fid-* (the bead sample without --fid-density: 0.3 per µm²), the slide's --slide-*.
webSMLM block	CellField.buildWindow(w, h, { specimen: 'Nanorulers', params: { origamiDensity: 0.5, ... } }).

What a switch does:

• It is a new sample. In Micro-Manager the illumination history (where the sample was lit, so bleached or activated) and the sample's drift start afresh, the same as after a new seed. Switching back gives the first sample again, as it was before it was ever lit.
• The focus stays. The cell field's start focus is 0.5 µm above the coverslip; the nanorulers' dyes lie 13.5 nm above it, so set the ZStage (the viewer's Focus height) to about 0 - 0.02 µm for them, and the bead sample's beads a radius above it (0.05-0.1 µm). The CLI focuses on the docking strands, or the beads, by itself when --z is not given.
• The bead sample brings beads. Mounting it while no beads are set (density 0) sets 0.3 per µm², while the aggregation is 0 sets 40 %, and moves beads set to sit on top of the sample to the coverslip (Micro-Manager and the viewer; the CLI when --fid-density or --fid-aggregation-pct is not given). Its light is 561 nm at 0.1 kW/cm², the other lasers off.
• The fluorescent slide brings its light. Mounting it in the viewer sets its dye's channel at 0.02 kW/cm² (the default mix: 561 nm), the other lasers off; in Micro-Manager that is the Lasers preset Auto (a mount keeps the lasers as set). Its layer looks the same at any focus.
• Each sample keeps its settings. The cell field's and the nanorulers' properties and labels exist side by side; switching changes none of them. The camera's gain preset and the light path follow the mounted sample's labels (the light path: every labelled target's preset combined, light-preset auto; the bead sample: its own, Beads-561; the slide: its dye's, Slide-561 for the mix).
• BrightField shows only what the sample's geometry gives it (optics): the cells' refractive index. DNA origami 13 nm thick gives no contrast at these NAs, so the nanorulers' BrightField frames hold the lamp and the camera noise only; so do the bead sample's and the fluorescent slide's.

Adding a sample (a new geometry in the core, its registry entry, its Micro-Manager device): see Extending.