Micro-Manager¶
A simulated microscope for Micro-Manager: a device adapter whose camera images the same sample as the viewer -- a field of cells or DNA-origami nanorulers -- live, as you move the stage, change the focus, switch channels or open the shutters. Windows x64.
Which Micro-Manager
The adapter needs a Micro-Manager 2.0 nightly build from 21 February 2026 or later (device interface 75): nightly builds. Older builds refuse the DLL. From Python: a pymmcore for device interface 75 (12.5.0.75.x; pymmcore-plus installs it).
Download the adapter Basic configuration
Every file of a release (the Advanced and Expert configurations, the DLL's .sha256, the build info) is on the
releases page. The DLL is GPL-3.0 (its licence files are on the
releases page too); see Building to build it
yourself.
Getting started¶
- Install a Micro-Manager 2.0 nightly build (21 February 2026 or later).
- Copy
mmgr_dal_inSiliScope.dllandinSiliScope_Basic.cfginto your Micro-Manager folder (for exampleC:\Program Files\Micro-Manager-2.0). - Start Micro-Manager and load
inSiliScope_Basic.cfgas the hardware configuration. - Press Live: you see the cell field at the coverslip, 0.5 um above it. Move the XY stage to go elsewhere in the field, the Z stage to focus (its position is the focal plane's height above the coverslip).
- Pick a Channel (the label mode and its dye:
AF647 dSTORM,mEos3.2 PALM,ATTO655 DNA-PAINT,mEGFP WideField,BrightField), an Illumination (Epi / HILO / TIRF) and a Quality (Fast / Realistic / Exhaustive). The Specimen group mounts the nanorulers instead of the cells. - Acquire as with a real microscope: snaps, live, sequences and hardware z stacks. Imaging bleaches where you look.
From Python, with pymmcore-plus:
from pymmcore_plus import CMMCorePlus
core = CMMCorePlus()
core.setDeviceAdapterSearchPaths([r"C:\Program Files\Micro-Manager-2.0"])
core.loadSystemConfiguration(r"C:\Program Files\Micro-Manager-2.0\inSiliScope_Basic.cfg")
core.setConfig("Channel", "ATTO655 DNA-PAINT")
core.snapImage(); img = core.getImage()
inSiliScope_Advanced.cfg and inSiliScope_Expert.cfg show more of the microscope (filter wheels, every property).
The Quickstart walks through the configuration groups, the targets and their labels,
the shutters and the caches in more detail.
Devices and properties¶
The inSiliScope adapter is a hub (inSiliScope) with one device per part of the microscope. Every property has a
tier: the hub's pre-init Detail (Basic, Advanced or Expert) decides which tiers a session shows; a property
above it is not created and keeps its default. The shipped configurations adapter/inSiliScope/config/inSiliScope_{Basic,Advanced,Expert}.cfg
load the devices with their config groups (Channel, Objective, Aberrations, Camera, Quality, Drift, Specimen,
Illumination, BfpPosition (Advanced and up), the 561 and 640 nm laser powers) and pixel-size calibrations. Where a new property belongs, and the rules behind the tiers: spec/MM_DEVICES.md in the repository.
Micro-Manager's own properties (Exposure, Binning, State, Label, Position, ...) are not listed.
| Device | Type | Tier | What it is |
|---|---|---|---|
Hub |
Hub | Basic | inSiliScope: a simulated fluorescence/BrightField microscope (hub of its devices) |
Camera |
Camera | Basic | inSiliScope camera: a simulated sCMOS/EMCCD |
XYStage |
XYStage | Basic | Moves the field of view over the sample |
ZStage |
Stage | Basic | The focus: height of the focal plane above the coverslip (um) |
Objective |
State | Basic | Objective turret: NA, immersion, magnification, aberrations |
EmissionPath |
Magnifier | Basic | Magnification between objective and camera (sets the pixel size) |
FilterCube |
State | Basic | Filter cube: excitation filter, dichroic and emission filter as one choice |
ExcitationFilter |
State | Advanced | Laser clean-up filter wheel (the cube's excitation filter, set on its own) |
Dichroic |
State | Advanced | Dichroic mirror wheel (the cube's dichroic, set on its own) |
EmissionFilter |
State | Advanced | Emission filter wheel (the cube's emission filter, set on its own) |
Lasers |
Shutter | Basic | Laser engine and its shutter: line powers, beam profile, geometry |
TransmittedLamp |
Shutter | Basic | Transmitted-light lamp and its shutter (BrightField) |
SampleHolder |
State | Basic | The mounted specimen; drift and background of the sample |
CellField |
Generic | Basic | Specimen: a field of cells with their labelled structures |
Nanorulers |
Generic | Basic | Specimen: DNA-origami nanorulers on the coverslip (mount them with SampleHolder) |
Fiducials |
Generic | Basic | Fiducial beads on the sample (any specimen): type, density, size, height |
FluorescentSlide |
Generic | Basic | Specimen: a fluorescent slide, a uniform dye layer (mount it with SampleHolder) |
Fluorophores |
Generic | Basic | The dyes: label mode, photophysics readouts, custom dyes |
Renderer |
Generic | Basic | How the images are computed: quality, GPU, caches, numerics |
Hub¶
inSiliScope: a simulated fluorescence/BrightField microscope (hub of its devices).
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
Detail |
pre-init | Basic | Advanced, Basic, Expert |
set before the devices initialize |
RandomSeed |
pre-init | 42 | set before the devices initialize | |
Version |
Basic | 0.1.0 | the release (read-only) |
Camera¶
inSiliScope camera: a simulated sCMOS/EMCCD.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
FovSize |
pre-init | 256x256 | 1024x1024 (slow, ~4x the memory of 512), 128x128, 256x256, 512x512 (slower) |
set before the devices initialize |
CameraPreset |
Basic | Kinetix22 | Kinetix22, iXonUltra897, Custom |
A camera model: sets the sensor type, QE curve, noise values, gain and sensor pixel. |
PixelSizeNm |
Advanced (read-only) | 97.45127436 | The pixel size in the sample: SensorPixelUm / (objective x emission magnification). | |
SensorPixelUm |
Advanced | 6.5 | 0.5 .. 50 | The sensor's physical pixel pitch (um); the camera preset sets it. |
CameraType |
Advanced | sCMOS | sCMOS, EMCCD |
The noise chain: sCMOS (per-pixel maps) or EMCCD (gain register, CIC); the camera preset sets it. |
QuantumEfficiency |
Advanced | 0.85 | 0.01 .. 1 | The QE where the QE curve is Flat (and for BrightField without a curve). |
QeCurve |
Advanced | Kinetix22 | Kinetix22, iXonUltra897, Custom |
The QE curve the detected fractions use (a camera's FPbase curve, or Custom = flat). |
GainElectronsPerADU |
Advanced | 0.25 | 0.0001 .. 100 | Conversion gain, electrons per ADU, per photoelectron (an EMCCD's includes its EM gain). |
OffsetADU |
Advanced | 100 | 0 .. 10000 | The camera offset (ADU). |
OffsetStdADU |
Advanced | 0.5 | 0 .. 500 | The pixel-to-pixel spread of the offset (ADU, a static pattern). |
ReadNoiseElectrons |
Advanced | 1.2 | 0 .. 100 | Read noise, electrons RMS (an EMCCD's before the gain register). |
DarkCurrentElectronsPerSec |
Advanced | 1.03 | 0 .. 100 | Dark current, electrons per pixel per second. |
sCMOS_GainStdPctPerPixel |
Expert | 0.5 | 0 .. 50 | sCMOS only: pixel-to-pixel spread of the gain, % (a static pattern). |
sCMOS_ReadNoiseStdPctPerPixel |
Expert | 20 | 0 .. 100 | sCMOS only: pixel-to-pixel spread of the read noise, %. |
EMCCD_CicElectrons |
Expert | 0.002 | 0 .. 1 | EMCCD only: clock-induced charge, electrons per pixel per frame. |
EMCCD_EmGain |
Expert (read-only) | 4 | EMCCD only: the EM gain, the preset's pre-amplifier sensitivity / the gain (read-only). | |
BitDepth |
Expert | 16 | 8 .. 16 | The ADC's bit depth (the EMCCD path clips to it). |
XYStage¶
Moves the field of view over the sample.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
StageSpeedUmPerSec |
Advanced | 5000 | 1 .. 100000 | Speed of a stage move, um/s. |
StageSettleMs |
Advanced | 20 | 0 .. 10000 | Time the stage stays busy after arriving, ms. |
StageLimitUm |
Advanced | 1000000 | Travel limit, +/- um around the origin. |
Objective¶
Objective turret: NA, immersion, magnification, aberrations.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
ZernikePreset |
Basic | MixedRealisticObjective | None, AstigmatismWeak, AstigmatismModerate, AstigmatismStrong, ComaWeak, ComaStrong, SphericalWeak, SphericalStrong, TrefoilModerate, MixedRealisticObjective, SaddlePoint, ExtendedRange, ExtendedRangeStrong |
The objective's aberrations: a named Zernike set (sets ZernikeCoefficients). |
NA |
Advanced | 1.4 | 0.1 .. 1.7 | Numerical aperture (setting it by hand makes the turret position Custom). |
ImmersionIndex |
Advanced | 1.518 | 1 .. 2 | Refractive index of the immersion medium. |
Magnification |
Advanced | 100 | 1 .. 250 | The objective's magnification (the pixel size follows; with the tube length, the pupil's geometry: a beam's spot size and entry tilt map to the sample through the focal length tube length / magnification). |
PsfKernelHalfWidthNm |
Advanced | 7000 | 100 .. 20000 | Half-width of the rendered PSF window (nm; a minimum, grown to cover the first Airy ring). |
PsfZRangeUm |
Advanced | 7 | 0.1 .. 20 | The z span of the PSF kernel (um): dyes further from focus use its end plane. |
PsfZStepUm |
Advanced | 0.1 | 0.01 .. 1 | The z step of the PSF kernel's planes (um). |
TubeLengthMm |
Expert | 200 | 50 .. 500 | The tube lens' focal length (mm): the objective's focal length is it over the magnification, the back focal plane's radius that x NA (a beam's spot size and tilt map to the sample through it). |
ZernikeCoefficients |
Expert | 0 0 0 0 0.05 0.08 0 0.06 0 0 0 0 0.07 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | The pupil's Zernike coefficients, OSA 0-27, in waves, space-separated (GibsonLanniZernike). | |
WorkingDistanceUm |
Expert | 150 | 0 .. 9999 | Working distance (um; the JVM GibsonLanni model only). |
EmissionPath¶
Magnification between objective and camera (sets the pixel size).
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
EmissionMagnification |
Basic | 0.667 | 0.1 .. 10 | Magnification between the objective and the camera (tube lens / relay; goes with the camera). |
ExcitationFilter¶
Laser clean-up filter wheel (the cube's excitation filter, set on its own).
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
CustomLoNm |
Expert | 635 | 300 .. 900 | The Custom excitation filter's lower edge (nm). |
CustomHiNm |
Expert | 645 | 300 .. 900 | The Custom excitation filter's upper edge (nm). |
Dichroic¶
Dichroic mirror wheel (the cube's dichroic, set on its own).
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
CustomEdgeNm |
Expert | 650 | 300 .. 900 | The Custom dichroic's edge (nm; a long pass). |
EmissionFilter¶
Emission filter wheel (the cube's emission filter, set on its own).
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
CustomLoNm |
Expert | 657.5 | 300 .. 900 | The Custom emission filter's lower edge (nm). |
CustomHiNm |
Expert | 694.5 | 300 .. 900 | The Custom emission filter's upper edge (nm). |
Lasers¶
Laser engine and its shutter: line powers, beam profile, geometry.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
Laser405KWcm2 |
Basic | 0 | 0 .. 10 | Intensity of this laser line at the sample, kW/cm^2 (0 = off). |
Laser488KWcm2 |
Basic | 0 | 0 .. 10 | Intensity of this laser line at the sample, kW/cm^2 (0 = off). |
Laser561KWcm2 |
Basic | 1 | 0 .. 10 | Intensity of this laser line at the sample, kW/cm^2 (0 = off). |
Laser640KWcm2 |
Basic | 1 | 0 .. 10 | Intensity of this laser line at the sample, kW/cm^2 (0 = off). |
Laser730KWcm2 |
Basic | 0 | 0 .. 10 | Intensity of this laser line at the sample, kW/cm^2 (0 = off). |
Preset |
Basic | Auto | None, Auto, dSTORM-640, dSTORM-561, dSTORM-488, PAINT-640, PAINT-561, PAINT-488, PALM-561, PALM-primed, WF-405, WF-488, WF-561, WF-640, Beads-561, Slide-405, Slide-488, Slide-561, Slide-640 |
A light path (lasers + filter cube). Auto: the labelled targets' dyes' presets together (each laser line at its highest power; the multi-band filter set where their filters differ), what a dye or mode pick applies. A preset by name: one dye mode's. None = as set. |
IlluminationProfile |
Basic | Gaussian | Flat, Gaussian, FlatTop |
The excitation beam's cross-section: Flat, Gaussian or FlatTop (a disc with a soft edge). |
IlluminationFwhmPct |
Basic | 100 | 10 .. 300 | The beam's FWHM (Gaussian, FlatTop), % of the field of view's width. |
BfpPosition |
Basic | 0.95 | 0 .. 1.2 | Where the laser spot sits in the objective's back focal plane: 0 = its centre (epi), 1 = the critical angle; between: HILO (an inclined sheet), above: TIRF (an evanescent layer), up to the pupil edge NA / medium index (beyond it no light reaches the sample). |
Pattern |
Basic | Off | Off, SIM2D, SIM3D, LatticeSIM2D, LatticeSIM3D, Custom |
Structured illumination: the light as coherent beams in the back focal plane, the fringes stepping with the frame. Off: one beam at BfpPosition. SIM2D: two beams at +-BfpPosition, 3 phases x 3 orientations. SIM3D: + the centre beam, 5 phases x 3 orientations. LatticeSIM2D: +-x and +-y, 9 phases. LatticeSIM3D: + the centre, 13 phases (the pairs stepping 2:3). Custom: the Beams matrix alone. A pick sets BfpPosition to the type's radius (2D 0.95; 3D and the lattices 0.9) and PatternPolarization to S; past 1 the beams are evanescent (TIRF-SIM). The kinetics run on the pattern's cycle mean, each frame's image on its exact pattern. |
IlluminationRegime |
Advanced (read-only) | HILO | Epi, HILO, TIRF, or Clipped (the spot beyond the pupil edge: no light) (read-only). | |
IlluminationDepthNm |
Advanced (read-only) | 14973.57262 | TIRF: the evanescent field's 1/e intensity depth at the first label's main line; HILO: the sheet's thickness on the axis; -1 in epi (nm, read-only). | |
CustomLineNm |
Advanced | 0 | 0 .. 1000 | Wavelength of an extra laser line (nm). |
CustomLineKWcm2 |
Advanced | 0 | 0 .. 10 | Intensity of the extra line, kW/cm^2. |
ChamberHeightUm |
Advanced | 100 | 0 .. 1000 | Depth of the imager solution over the coverslip (um): the DNA-PAINT free-imager background is its column of light (epi: all of it; HILO: about the sheet; TIRF: about the penetration depth). |
PatternPolarization |
Advanced | S | S, P, Circular, LinearX, Unpolarized |
Every beam's polarization: S (across its plane of incidence: full fringe contrast; the lattice's x and y pairs then do not interfere, LatticeSIM3D's centre beam is linear diagonal), P, Circular, LinearX (the pupil field along the lab x axis) or Unpolarized (the mean of the S and P patterns). A Pattern pick sets S. |
PatternAnchor |
Advanced | Focus | Focus, Coverslip |
The plane the beams are in phase at, which the pattern's axial structure is fixed to: Focus (a grating or SLM conjugate to the focal plane: the fringes move with the focus and the sample moves through them, by the stage or the objective alike) or Coverslip (the fringes fixed to the sample: an illumination that does not move with the focus). The evanescent decay is from the coverslip either way. |
PatternPhases |
Advanced | 0 | 0 .. 64 | Phase steps per orientation (0 = the type's: 3, 5, 9, 13). |
PatternAngles |
Advanced | 0 | 0 .. 12 | Orientations per cycle, 180 / n degrees apart (0 = the type's: 3 for SIM2D and SIM3D, 1 for the lattices). |
PatternOrder |
Advanced | AngleMajor | AngleMajor, PhaseMajor |
The frame program's order: AngleMajor (every phase of an orientation, then the next orientation) or PhaseMajor. |
PatternAngle0Deg |
Advanced | 0 | -180 .. 180 | The first orientation, degrees from the x axis. |
PatternPhase0 |
Advanced | 0 | -100 .. 100 | Added to the phase index (fractional allowed): the pattern's starting phase. |
PatternCentreAmp |
Advanced | 1 | 0 .. 10 | The centre beam's field amplitude over the side beams' (SIM3D, LatticeSIM3D; 1, an estimate). |
PatternFrame |
Advanced (read-only) | 0 | The sample's pattern frame counter: the index the next taken frame has in the frame program (every taken frame counts, dark ones too; a sequence start sets it to 0 under PatternRestart = Sequence); each live frame's metadata tag inSiliScope-PatternFrame is the index it was rendered with (read-only). | |
PatternRestart |
Advanced | Sequence | Sequence, Never |
When the pattern frame counter restarts at 0: at every sequence start (Live, an acquisition: its frames aligned with the program) or never (the counter runs on across acquisitions). |
PatternState |
Advanced (read-only) | no pattern | The frame program's state the next taken frame has: 'angle a phase p, frame f of N' (read-only). | |
PatternPeriodNm |
Advanced (read-only) | -1 | The lateral fringe period of the pattern at the first label's main line (nm; the largest of several; -1 without a pattern) (read-only). | |
SpotRadiusUm |
Advanced (read-only) | 19.22916107 | The beam's spot in the back focal plane: the Gaussian spot's 1/e^2 radius (um) that makes the envelope of IlluminationFwhmPct at the strongest line (a Fourier pair through the objective's focal length) (read-only). | |
PatternPhaseDriftTurnsPerSqrtSec |
Expert | 0 | 0 .. 10 | Each beam's phase takes a random walk: its RMS after 1 s (turns; per seed and frame, as the sample drift). 0 = none. |
PatternPhaseDriftTurnsPerSec |
Expert | 0 | -100 .. 100 | Each beam's phase drifts at its phase step x this (turns/s): the pattern slides along its stepping direction. 0 = none. |
Beams |
Expert | 0.95 0 0 0 0 1 0 -999 0 0 0 | Every beam of the illumination, one row per beam, rows separated by ';', columns separated by spaces: ux uy spot tiltX tiltY amp phase pol ellip phaseStep nm -- the position in the back focal plane (u units: 1 = the critical angle, beyond it evanescent), the spot's 1/e^2 radius in the pupil (um; 0 = from IlluminationFwhmPct: a Gaussian spot of radius w makes an envelope of 1/e^2 radius lambda f / (pi w), f = TubeLengthMm / Magnification), the bundle's entry tilt (degrees, two axes: the envelope's centre moves by f tan tilt), the field amplitude, the phase (turns), the polarization angle (degrees; 0 s, 90 p; below -180 unpolarized), the ellipticity phase (turns; 0.25 circular), the phase step per phase index (1 / PatternPhases turns) and the laser line the beam carries (nm; 0 = every line). Off shows its one beam; a Pattern its beams; an edit replaces them (Custom: the matrix alone). Example, a 2D SIM pair at 0.95: 0.95 0 0 0 0 1 0 0 0 1 0; -0.95 0 0 0 0 1 0 0 0 -1 0 |
TransmittedLamp¶
Transmitted-light lamp and its shutter (BrightField).
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
IntensityPhotonsPerPxPerSec |
Basic | 80000 | 0 .. 1000000000 | Photons per pixel per second through an empty field. |
CondenserNA |
Advanced | 0.4 | 0 .. 1.5 | Condenser numerical aperture (the partial coherence of the illumination). |
WavelengthNm |
Advanced | 550 | 300 .. 1000 | The lamp's (filtered) wavelength, nm. |
UseObjectiveAberrations |
Expert | 1 | 0 .. 1 | 1: the detection pupil carries the objective's Zernike aberrations. |
SampleHolder¶
The mounted specimen; drift and background of the sample.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
DriftPreset |
Basic | Off | Off, Low, Medium, High, Extreme, Custom |
How much the sample drifts: sets the xy and z drift speeds (0, 2, 5, 25, 250 nm/s) and random walks (0, 0.4, 1, 5, 50 nm/sqrt s). Custom = as set. |
TimeWhileIdle |
Basic | Running | Running, Paused |
Between acquisitions: Running = the sample drifts on and an opened lasers' shutter keeps lighting it (bleaching, activating); Paused = nothing changes until the next frame is acquired. |
MediumIndex |
Advanced | 1.337 | 1 .. 2 | Refractive index of the medium over the coverslip (BrightField; the critical angle of Lasers.BfpPosition). |
DriftXySpeedNmPerSec |
Advanced | 0 | 0 .. 1000 | Directed sample drift in xy, mean speed (nm/s). |
DriftZSpeedNmPerSec |
Advanced | 0 | 0 .. 1000 | Directed sample drift in z, mean speed (nm/s); its direction: DriftZDirection. |
DriftXyNmPerSqrtSec |
Advanced | 0 | 0 .. 200 | Random-walk drift in x and y: RMS displacement after 1 s (nm), per axis. |
DriftZNmPerSqrtSec |
Advanced | 0 | 0 .. 200 | Random-walk drift in z: RMS displacement after 1 s (nm). |
BackgroundPhotonsPerSec |
Advanced | 0 | 0 .. 200000 | Uniform background (autofluorescence, out-of-focus light), photons per pixel per second. |
BackgroundDecaySec |
Advanced | 0 | 0 .. 100000 | The background fades to 30% with this time constant (s; 0 = no fade). |
DriftXyAngleDeg |
Expert | -1 | -1 .. 360 | Direction of the directed xy drift (deg; -1 = random per seed). |
DriftZDirection |
Expert | Random | Random, Up, Down |
Direction the z drift starts in: Up = away from the coverslip, Down = towards it, Random = per seed. |
DriftXyAngleWanderDeg |
Expert | 180 | 0 .. 180 | The xy drift direction swings slowly within +/- this (deg; 180 = any direction). |
DriftZAngleWanderDeg |
Expert | 90 | 0 .. 180 | The z drift swings within +/- this (deg): speed x cos(angle); 90 = between full speed and still, 180 = also back. |
DriftSpeedWanderPct |
Expert | 0 | 0 .. 100 | RMS wander of the drift speeds, % of the mean. |
DriftWanderTimeSec |
Expert | 60 | 0.1 .. 100000 | Correlation time of the wanders (s). |
PsfSampleIndex |
Expert | 1.518 | 1 .. 2 | Refractive index of the sample medium in the Gibson-Lanni PSF (= immersion: no mismatch). |
PsfSampleDepthNm |
Expert | 0 | -100000 .. 100000 | Depth of the emitters below the coverslip in the Gibson-Lanni PSF (nm). |
CellField¶
Specimen: a field of cells with their labelled structures.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
Microtubules_Mode |
Basic | DNA-PAINT | dSTORM, PALM, DNA-PAINT, WideField |
How the microtubules' dye emits (each target has its own): dSTORM, PALM, DNA-PAINT or WideField. A change sets the labelled % to the mode's suggestion and the label to Typical where the dye has no data for it. |
Microtubules_Label |
Basic | Typical | Typical, ATTO655, ATTO542, Cy3B, Custom, Dye1, Dye2, Dye3, None |
The label: Typical (the usual dye for this target's Mode), any dye with data in that mode (Dye1-3: the custom dyes of Fluorophores, Expert), or None (no label: the target is off). A pick applies the Lasers Auto preset. |
NuclearPores_Mode |
Basic | DNA-PAINT | dSTORM, PALM, DNA-PAINT, WideField |
How the nuclear pores' dye emits (each target has its own): dSTORM, PALM, DNA-PAINT or WideField. A change sets the labelled % to the mode's suggestion and the label to Typical where the dye has no data for it. |
NuclearPores_Label |
Basic | Typical | Typical, ATTO655, ATTO542, Cy3B, Custom, Dye1, Dye2, Dye3, None |
The label: Typical (the usual dye for this target's Mode), any dye with data in that mode (Dye1-3: the custom dyes of Fluorophores, Expert), or None (no label: the target is off). A pick applies the Lasers Auto preset. |
Microtubules_LabelingPct |
Advanced | 70 | 0 .. 100 | Labelled fraction of the microtubules' sites, % (a mode change sets its suggestion). |
Microtubules_ImagerNanoMol |
Advanced | 1 | 0 .. 10000 | DNA-PAINT imager concentration in the buffer, nanomolar: binding events per site per second = k_on x c, so it sets how many sites blink per frame (a change acts at once); the free imager adds a uniform background. |
Microtubules_BoundTimeSec |
Advanced | 0.05 | 0.001 .. 100 | DNA-PAINT: mean time an imager stays bound to a docking site, s (exponential; half-time = 0.693 x this). A property of the docking/imager sequence, so of the target, not of the dye. |
Microtubules_KonPerMolarPerSec |
Advanced | 1000000 | 0 .. 1000000000 | DNA-PAINT: imager association rate k_on, per molar per second; binding events per site per second = k_on x the imager concentration. |
Microtubules_Binder |
Advanced | IgG2-PAINT | Legacy, IgG2-STORM, IgG1-STORM, IgG2-PAINT, IgG1-PAINT, Nanobody, Nanobody-PAINT, SNAP-Halo, FP |
How the microtubules' dye is attached: the probe (antibodies, nanobody, SNAP/Halo tag, FP fusion; with or without a DNA-PAINT docking strand) sets the dye's distance from the structure. Legacy: the built-in numbers before the linkage model. |
NuclearPores_LabelingPct |
Advanced | 60 | 0 .. 100 | Labelled fraction of the nuclear pores' sites, % (a mode change sets its suggestion). |
NuclearPores_ImagerNanoMol |
Advanced | 2.5 | 0 .. 10000 | DNA-PAINT imager concentration in the buffer, nanomolar: binding events per site per second = k_on x c, so it sets how many sites blink per frame (a change acts at once); the free imager adds a uniform background. |
NuclearPores_BoundTimeSec |
Advanced | 0.05 | 0.001 .. 100 | DNA-PAINT: mean time an imager stays bound to a docking site, s (exponential; half-time = 0.693 x this). A property of the docking/imager sequence, so of the target, not of the dye. |
NuclearPores_KonPerMolarPerSec |
Advanced | 1000000 | 0 .. 1000000000 | DNA-PAINT: imager association rate k_on, per molar per second; binding events per site per second = k_on x the imager concentration. |
NuclearPores_Binder |
Advanced | SNAP-Halo | Legacy, IgG2-STORM, IgG1-STORM, IgG2-PAINT, IgG1-PAINT, Nanobody, Nanobody-PAINT, SNAP-Halo, FP |
How the nuclear pores' dye is attached: the probe (antibodies, nanobody, SNAP/Halo tag, FP fusion; with or without a DNA-PAINT docking strand) sets the dye's distance from the structure. Legacy: the built-in numbers before the linkage model. |
NuclearLamina_Mode |
Advanced | DNA-PAINT | dSTORM, PALM, DNA-PAINT, WideField |
How the nuclear lamina' dye emits (each target has its own): dSTORM, PALM, DNA-PAINT or WideField. A change sets the labelled % to the mode's suggestion and the label to Typical where the dye has no data for it. |
NuclearLamina_Label |
Advanced | None | Typical, ATTO655, ATTO542, Cy3B, Custom, Dye1, Dye2, Dye3, None |
The label: Typical (the usual dye for this target's Mode), any dye with data in that mode (Dye1-3: the custom dyes of Fluorophores, Expert), or None (no label: the target is off). A pick applies the Lasers Auto preset. |
NuclearLamina_LabelingPct |
Advanced | 70 | 0 .. 100 | Labelled fraction of the nuclear lamina' sites, % (a mode change sets its suggestion). |
NuclearLamina_ImagerNanoMol |
Advanced | 2.5 | 0 .. 10000 | DNA-PAINT imager concentration in the buffer, nanomolar: binding events per site per second = k_on x c, so it sets how many sites blink per frame (a change acts at once); the free imager adds a uniform background. |
NuclearLamina_BoundTimeSec |
Advanced | 0.05 | 0.001 .. 100 | DNA-PAINT: mean time an imager stays bound to a docking site, s (exponential; half-time = 0.693 x this). A property of the docking/imager sequence, so of the target, not of the dye. |
NuclearLamina_KonPerMolarPerSec |
Advanced | 1000000 | 0 .. 1000000000 | DNA-PAINT: imager association rate k_on, per molar per second; binding events per site per second = k_on x the imager concentration. |
NuclearLamina_Binder |
Advanced | IgG2-PAINT | Legacy, IgG2-STORM, IgG1-STORM, IgG2-PAINT, IgG1-PAINT, Nanobody, Nanobody-PAINT, SNAP-Halo, FP |
How the nuclear lamina' dye is attached: the probe (antibodies, nanobody, SNAP/Halo tag, FP fusion; with or without a DNA-PAINT docking strand) sets the dye's distance from the structure. Legacy: the built-in numbers before the linkage model. |
CellDiameterMinUm |
Advanced | 25 | 5 .. 100 | Smallest cell diameter, um. |
CellDiameterMaxUm |
Advanced | 35 | 5 .. 100 | Largest cell diameter, um. |
Occupancy |
Advanced | 0.33 | 0.05 .. 1 | Fraction of the coverslip covered by cells. |
MicrotubuleDensityPerUm2 |
Advanced | 0.9 | 0 .. 2 | Microtubule density, per um^2 of cell. |
NuclearPoreDensityPerUm2 |
Advanced | 8 | 0 .. 30 | Nuclear pore complexes per um^2 of nuclear envelope, over the whole envelope (8; measured 5-8.6 in HeLa and U2OS nuclei; 0 = no pores, the target is off). |
NuclearLaminaDensityPerUm2 |
Advanced | 2000 | 100 .. 10000 | Nuclear lamina points per um^2 of nuclear envelope, uniform by area (2000, an estimate: a random stand-in for the lamin network). Unlabelled by default: NuclearLamina_Label turns it on. |
IndexCytoplasm |
Advanced | 1.35 | 1 .. 2 | Refractive index of the cytoplasm (BrightField). |
IndexNucleus |
Advanced | 1.35 | 1 .. 2 | Refractive index of the nucleus (BrightField). |
IndexMicrotubule |
Advanced | 1.48 | 1 .. 2 | Refractive index of a microtubule (BrightField). |
Microtubules_BinderNm |
Expert | -1 | -1 .. 1000 | The probe's length from the binding site, outward along the structure's axis, nm (-1 = the Binder preset's). |
Microtubules_BinderFlexNm |
Expert | -1 | -1 .. 1000 | The probe's flexibility: its end lies in a ball of this radius, nm (-1 = the preset's). |
Microtubules_LinkerMinNm |
Expert | -1 | -1 .. 1000 | Shortest chemical linker from the probe to the dye, nm (-1 = the preset's). |
Microtubules_LinkerMaxNm |
Expert | -1 | -1 .. 1000 | Longest linker, nm (uniform in volume between the two; -1 = the preset's). |
NuclearPores_BinderNm |
Expert | -1 | -1 .. 1000 | The probe's length from the binding site, outward along the structure's axis, nm (-1 = the Binder preset's). |
NuclearPores_BinderFlexNm |
Expert | -1 | -1 .. 1000 | The probe's flexibility: its end lies in a ball of this radius, nm (-1 = the preset's). |
NuclearPores_LinkerMinNm |
Expert | -1 | -1 .. 1000 | Shortest chemical linker from the probe to the dye, nm (-1 = the preset's). |
NuclearPores_LinkerMaxNm |
Expert | -1 | -1 .. 1000 | Longest linker, nm (uniform in volume between the two; -1 = the preset's). |
NuclearLamina_BinderNm |
Expert | -1 | -1 .. 1000 | The probe's length from the binding site, outward along the structure's axis, nm (-1 = the Binder preset's). |
NuclearLamina_BinderFlexNm |
Expert | -1 | -1 .. 1000 | The probe's flexibility: its end lies in a ball of this radius, nm (-1 = the preset's). |
NuclearLamina_LinkerMinNm |
Expert | -1 | -1 .. 1000 | Shortest chemical linker from the probe to the dye, nm (-1 = the preset's). |
NuclearLamina_LinkerMaxNm |
Expert | -1 | -1 .. 1000 | Longest linker, nm (uniform in volume between the two; -1 = the preset's). |
ChunkSizeUm |
Expert | 26 | 4 .. 200 | Size of a packing block, um. |
FocusHeightUm |
Expert | 0 | -10 .. 10 | Extra focus offset above the coverslip, um. |
ZRangeUm |
Expert | 7 | 0 .. 50 | Total z slab around the focal plane whose dyes are rendered, um (0 = all). |
NucBaseMinUm |
Expert | 0.4 | 0 .. 2 | Nucleus base height, minimum (um). |
NucBaseMaxUm |
Expert | 0.9 | 0 .. 2 | Nucleus base height, maximum (um). |
NucIrregMin |
Expert | 0.03 | 0 .. 0.3 | Nucleus outline irregularity, minimum. |
NucIrregMax |
Expert | 0.2 | 0 .. 0.3 | Nucleus outline irregularity, maximum. |
NucBendMin |
Expert | 0 | 0 .. 1 | Nucleus kidney bend, minimum. |
NucBendMax |
Expert | 0.3 | 0 .. 1 | Nucleus kidney bend, maximum. |
NucSmooth |
Expert | 2.5 | 0 .. 4 | Nucleus outline smoothness (spectral exponent). |
NucThickIrreg |
Expert | 0.1 | 0 .. 0.4 | Nucleus thickness irregularity. |
NucAsym |
Expert | 0.5 | -0.9 .. 0.9 | Nucleus base widening. |
NucWidestMin |
Expert | 0.2 | 0 .. 1 | Height of the nucleus' widest point, minimum (fraction). |
NucWidestMax |
Expert | 0.4 | 0 .. 1 | Height of the nucleus' widest point, maximum (fraction). |
MicrotubuleStartDecayPct |
Expert | 1.6 | 0.05 .. 10 | Microtubule starts: decay length, % of the cell radius. |
MicrotubuleEndDecayPct |
Expert | 20 | 0.5 .. 50 | Microtubule ends: decay length, % of the cell radius. |
MicrotubuleDirKappa |
Expert | 1.5 | 0 .. 10 | Microtubule direction concentration (von Mises kappa). |
NuclearPoreMinDistNm |
Expert | 180 | 0 .. 500 | Smallest centre distance of two pores, nm (180; a pore is about 120 across). |
NuclearPoreRadiusNm |
Expert | 53.5 | 20 .. 150 | Radius of a pore's Nup96 rings, nm. |
NuclearPoreRingSepNm |
Expert | 50 | 0 .. 150 | Distance between a pore's cytoplasmic and nucleoplasmic ring, nm. |
NuclearPoreCornerSpreadNm |
Expert | 12 | 0 .. 30 | Diameter of the arc of 4 Nup96 at each of a ring's 8 corners, nm. |
NuclearLaminaPoreExclusionNm |
Expert | 40 | 0 .. 300 | Diameter of the lamina-free disc around each nuclear pore's centre, nm (40). |
Packing |
Expert | On | On, Off |
Relax the cells into a packed field (Off: their seeded positions). |
AbsorptionPerUm |
Expert | 0 | 0 .. 100 | Absorption of the cell material, per um (0 = unstained). |
Microtubules_Orientation |
Expert | Free | Free, Fixed, Random |
Dipole orientation of the microtubules' dyes. |
Microtubules_OrientPolarDeg |
Expert | 90 | 0 .. 180 | Fixed dipole: polar angle. |
Microtubules_OrientAzimuthDeg |
Expert | 0 | -360 .. 360 | Fixed dipole: azimuth. |
Microtubules_WobbleConeDeg |
Expert | 0 | 0 .. 90 | Dipole wobble cone half-angle. |
Microtubules_Motion |
Expert | Static | Static |
The dyes' motion. |
NuclearPores_Orientation |
Expert | Free | Free, Fixed, Random |
Dipole orientation of the nuclear pores' dyes. |
NuclearPores_OrientPolarDeg |
Expert | 90 | 0 .. 180 | Fixed dipole: polar angle. |
NuclearPores_OrientAzimuthDeg |
Expert | 0 | -360 .. 360 | Fixed dipole: azimuth. |
NuclearPores_WobbleConeDeg |
Expert | 0 | 0 .. 90 | Dipole wobble cone half-angle. |
NuclearPores_Motion |
Expert | Static | Static |
The dyes' motion. |
NuclearLamina_Orientation |
Expert | Free | Free, Fixed, Random |
Dipole orientation of the nuclear lamina' dyes. |
NuclearLamina_OrientPolarDeg |
Expert | 90 | 0 .. 180 | Fixed dipole: polar angle. |
NuclearLamina_OrientAzimuthDeg |
Expert | 0 | -360 .. 360 | Fixed dipole: azimuth. |
NuclearLamina_WobbleConeDeg |
Expert | 0 | 0 .. 90 | Dipole wobble cone half-angle. |
NuclearLamina_Motion |
Expert | Static | Static |
The dyes' motion. |
Nanorulers¶
Specimen: DNA-origami nanorulers on the coverslip (mount them with SampleHolder).
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
Docking_Mode |
Basic | DNA-PAINT | dSTORM, PALM, DNA-PAINT, WideField |
How the docking strands' dye emits (each target has its own): dSTORM, PALM, DNA-PAINT or WideField. A change sets the labelled % to the mode's suggestion and the label to Typical where the dye has no data for it. |
Docking_Label |
Basic | Typical | Typical, ATTO655, ATTO542, Cy3B, Custom, Dye1, Dye2, Dye3, None |
The label: Typical (the usual dye for this target's Mode), any dye with data in that mode (Dye1-3: the custom dyes of Fluorophores, Expert), or None (no label: the target is off). A pick applies the Lasers Auto preset. |
Design |
Basic | Nanoruler | Nanoruler, TUDelftLogo |
The DNA-origami design (data/origami/designs.json): Nanoruler = a 13 nm rod with three spots of docking strands SpacingNm apart and 20 nm ends; TUDelftLogo = a 2D origami, a rigid plate with one strand on each of 37 hexagons of the TU Delft logo, neighbours SpacingNm apart. |
SpacingNm |
Basic | 80 | 640, 320, 160, 80, 40, 20, 10, 5 |
Distance between neighbouring spots of docking strands, nm; the origami grows or shrinks with it (the nanoruler keeps its 20 nm ends: 80 nm = a 200 nm rod). |
DensityPerUm2 |
Basic | 1.2 | 0 .. 50 | Molecules per um^2 of coverslip, before the minimum spacing thins them. |
StrandsPerSpot |
Basic | 5 | 1 .. 5 | Docking strands per spot: ring positions 1..N of the nanoruler's 5 carry one (a 2D origami has 1). |
Docking_LabelingPct |
Advanced | 80 | 0 .. 100 | Labelled fraction of the docking strands' sites, % (a mode change sets its suggestion). |
Docking_ImagerNanoMol |
Advanced | 20 | 0 .. 10000 | DNA-PAINT imager concentration in the buffer, nanomolar: binding events per site per second = k_on x c, so it sets how many sites blink per frame (a change acts at once); the free imager adds a uniform background. |
Docking_BoundTimeSec |
Advanced | 0.2885390082 | 0.001 .. 100 | DNA-PAINT: mean time an imager stays bound to a docking site, s (exponential; half-time = 0.693 x this). A property of the docking/imager sequence, so of the target, not of the dye. |
Docking_KonPerMolarPerSec |
Advanced | 1000000 | 0 .. 1000000000 | DNA-PAINT: imager association rate k_on, per molar per second; binding events per site per second = k_on x the imager concentration. |
Bending |
Advanced | On | On, Off |
On: the rod bends in the coverslip plane as a worm-like chain (PersistenceLengthNm); Off: rigid. |
PersistenceLengthNm |
Advanced | 1500 | 10 .. 100000 | Bending persistence length, nm (an estimate: measured helix bundles 740 nm - 8.2 um). |
MinSpacingNm |
Advanced | 0 | 0 .. 5000 | No two molecule centres closer than this, nm (0 = no thinning). |
AttachHeightNm |
Advanced | 7 | 0 .. 1000 | Height of the rod's bottom above the glass (the surface coating), nm. |
LinkerNm |
Advanced | 3 | 0 .. 50 | A dye lies within this distance of its strand's anchor, outward, nm. |
Roll |
Advanced | Uniform | Uniform, Fixed |
How each rod landed about its own axis: Uniform = a random roll each, Fixed = RollDeg. |
RollDeg |
Advanced | 0 | -360 .. 360 | The fixed roll (Roll = Fixed), deg. |
KeepHeights |
Expert | Off | On, Off |
Off (2D): every strand at the rod axis height; On: the ring's own heights (3D, not validated yet). |
Docking_Orientation |
Expert | Free | Free, Fixed, Random |
Dipole orientation of the docking strands' dyes. |
Docking_OrientPolarDeg |
Expert | 90 | 0 .. 180 | Fixed dipole: polar angle. |
Docking_OrientAzimuthDeg |
Expert | 0 | -360 .. 360 | Fixed dipole: azimuth. |
Docking_WobbleConeDeg |
Expert | 0 | 0 .. 90 | Dipole wobble cone half-angle. |
Docking_Motion |
Expert | Static | Static |
The dyes' motion. |
Fiducials¶
Fiducial beads on the sample (any specimen): type, density, size, height.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
Type |
Basic | Gold | Gold, TetraSpeck, FluoSpheresOrange, FluoSpheresRed, FluoSpheresDarkRed, FluoSpheresInfrared, Nanodiamond |
The bead (data/fiducials, balinovic2019): Gold (100 nm, photoluminescence + scattered laser light), TetraSpeck (100 nm, four dyes), FluoSpheres Orange 540/560 (200 nm, for a 488 channel), Red 580/605 (200 nm), DarkRed 660/680 (200 nm; very bright at 640 nm), Infrared (100 nm), red Nanodiamond (100 nm). A pick sets DiameterNm to its product size. |
DensityPerUm2 |
Basic | 0 | 0 .. 100 | Beads per um^2 of coverslip, placed at random (Poisson: doublets happen); 0 = no beads. |
Height |
Basic | OnTop | Coverslip, OnTop, Layer |
Where the beads sit: Coverslip (on the glass, also under cells), OnTop (on the sample's surface; not on the bead sample, where it is the glass), Layer (anywhere in a gel layer of LayerUm, outside the cells). |
AggregationPct |
Basic | 0 | 0 .. 90 | The chance a bead is stuck to the next one, %: clumps of touching beads, n beads with probability (1 - p) p^(n-1) (mean 1 / (1 - p); at 10 %, 81 % of the beads are single); DensityPerUm2 counts beads (an estimate). |
DiameterNm |
Advanced | 100 | 10 .. 2000 | Mean bead diameter, nm (brightness ~ d^3: the dyes scale with the volume; the image is the PSF of the solid sphere); a Type pick sets its product size (100 or 200 nm; 20 nm beads: 20). |
DiameterCvPct |
Advanced | 12 | 0 .. 50 | Bead-to-bead diameter spread, % (normal; an estimate). |
LayerUm |
Advanced | 10 | 0 .. 1000 | The gel layer's thickness (Height = Layer), um. |
PsfZRangeUm |
Advanced | 14 | 0.1 .. 40 | Span of the beads' PSF z stack, um (Objective.PsfZRangeUm is the molecules'): a bead far off focus, on top of the cells or in a gel layer, keeps its defocused image. |
FarDefocus |
Expert | On | On, Off |
On: a bead beyond its PSF z stack is a blur growing with the defocus (a Gaussian matched to the stack's last plane, faded in over its last 0.5 um; not physical). Off: such beads are not drawn (faster with many beads far off focus). |
BleachHalfTimeSec |
Expert | 288 | 0 .. 1000000000 | A bead's fluorescence half-time at BleachRefKWcm2 at its dye's excitation peak, s (an estimate: 288 s; ~ 1 / the excitation; gold and nanodiamonds do not bleach; 0 = no bleaching). |
BleachRefKWcm2 |
Expert | 1 | 1e-06 .. 1000 | The intensity the half-time is given at, kW/cm^2. |
DyeCount |
Expert | -1 | -1 .. 1000000000 | Equivalent dyes (eps 1e5, QY 0.5) per bead of the type's reference diameter, every component; -1 = the type's (fitted to balinovic2019). |
BlockingOD |
Expert | 8 | 0 .. 12 | The emission path blocks a laser line by at least this optical density (gold's scattered laser light; ideal filters would block it fully). |
FluorescentSlide¶
Specimen: a fluorescent slide, a uniform dye layer (mount it with SampleHolder).
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
ThicknessUm |
Basic | 5 | 0 .. 1000 | The dye layer's thickness on the coverslip, um (5 um: the light of every height reaches the camera, collected defocused). |
Dye |
Basic | Mix | Mix, AF647, AF532, Cy5, ATTO655, ATTO542, Cy3B, mEos3.2, Dendra2, PAmCherry2, mEGFP, mScarlet, DAPI, Hoechst33342, Custom |
The layer's dye: Mix (TetraSpeck's four components, blue, green, orange and dark red, each at ConcentrationMicroMolar, as equivalent dyes) or a library dye. With the slide mounted, a pick applies the Lasers' Auto preset: the dye's channel at 0.02 kW/cm^2 (Mix: 561 nm). |
ConcentrationMicroMolar |
Basic | 10 | 0 .. 10000 | Each dye's concentration in the layer, uM (an estimate: 10 uM, ~8800 photons per pixel per 50 ms frame at the centre of the default 561 nm beam, 0.02 kW/cm^2, 5 um). |
BleachHalfTimeSec |
Basic | 900 | 0 .. 1000000000 | The layer's fluorescence half-time at 1 kW/cm^2 at its dye's excitation peak, s (an estimate: 900 s; ~ 1 / the excitation, so 12.5 h at 0.02 kW/cm^2; 0 = no bleaching). The bleaching follows the sample's light history pixel by pixel. |
Fluorophores¶
The dyes: label mode, photophysics readouts, custom dyes.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
Microtubules_EffectiveDye |
Advanced (read-only) | ATTO655 (DNA-PAINT) | The dye and mode the microtubules' label resolves to (Typical: the usual dye for the mode; read-only). | |
Microtubules_DetectedPct |
Advanced (read-only) | 70.20774444 | The microtubules' dye: % of its emission the light path detects (read-only). | |
Microtubules_EmissionNm |
Advanced (read-only) | 697.8311128 | The microtubules' dye: effective detected wavelength, nm (the PSF's; read-only). | |
Microtubules_PhotonsPerSecOn |
Advanced (read-only) | 74270.55856 | The microtubules' dye: detected photons per second while ON (read-only). | |
NuclearPores_EffectiveDye |
Advanced (read-only) | Cy3B (DNA-PAINT) | The dye and mode the nuclear pores' label resolves to (Typical: the usual dye for the mode; read-only). | |
NuclearPores_DetectedPct |
Advanced (read-only) | 49.42111786 | The nuclear pores' dye: % of its emission the light path detects (read-only). | |
NuclearPores_EmissionNm |
Advanced (read-only) | 607.3777953 | The nuclear pores' dye: effective detected wavelength, nm (the PSF's; read-only). | |
NuclearPores_PhotonsPerSecOn |
Advanced (read-only) | 136746.8708 | The nuclear pores' dye: detected photons per second while ON (read-only). | |
NuclearLamina_EffectiveDye |
Advanced (read-only) | Cy3B (DNA-PAINT) | The dye and mode the nuclear lamina' label resolves to (Typical: the usual dye for the mode; read-only). | |
NuclearLamina_DetectedPct |
Advanced (read-only) | 0 | The nuclear lamina' dye: % of its emission the light path detects (read-only). | |
NuclearLamina_EmissionNm |
Advanced (read-only) | 0 | The nuclear lamina' dye: effective detected wavelength, nm (the PSF's; read-only). | |
NuclearLamina_PhotonsPerSecOn |
Advanced (read-only) | 0 | The nuclear lamina' dye: detected photons per second while ON (read-only). | |
Docking_EffectiveDye |
Advanced (read-only) | ATTO655 (DNA-PAINT) | The dye and mode the docking strands' label resolves to (Typical: the usual dye for the mode; read-only). | |
Docking_DetectedPct |
Advanced (read-only) | 0 | The docking strands' dye: % of its emission the light path detects (read-only). | |
Docking_EmissionNm |
Advanced (read-only) | 0 | The docking strands' dye: effective detected wavelength, nm (the PSF's; read-only). | |
Docking_PhotonsPerSecOn |
Advanced (read-only) | 0 | The docking strands' dye: detected photons per second while ON (read-only). | |
Dye1_Source |
Expert | AF647 | AF647, AF532, Cy5, ATTO655, ATTO542, Cy3B, mEos3.2, Dendra2, PAmCherry2, mEGFP, mScarlet, DAPI, Hoechst33342, Custom |
The library dye this custom dye starts from. |
Dye1_FluorescentPct |
Expert | 100 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_Qy |
Expert | 0.33 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_ExtCoeff |
Expert | 270000 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_OnSec |
Expert | 0.02650544377 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_OffSec |
Expert | 52.9843821 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_BleachProb |
Expert | 0.07142857143 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_InitialOnSec |
Expert | 2 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_Activation405 |
Expert | 60 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_SpontActivation |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_Primed |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_PrePhotonBudget |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_PhotonCv |
Expert | 0.5 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye1_PhotonBudget |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_Source |
Expert | mEos3.2 | AF647, AF532, Cy5, ATTO655, ATTO542, Cy3B, mEos3.2, Dendra2, PAmCherry2, mEGFP, mScarlet, DAPI, Hoechst33342, Custom |
The library dye this custom dye starts from. |
Dye2_FluorescentPct |
Expert | 60 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_Qy |
Expert | 0.55 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_ExtCoeff |
Expert | 32200 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_OnSec |
Expert | 0.05 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_OffSec |
Expert | 0.5 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_BleachProb |
Expert | 0.5 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_InitialOnSec |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_Activation405 |
Expert | 1 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_SpontActivation |
Expert | 1e-05 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_Primed |
Expert | 0.01 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_PrePhotonBudget |
Expert | 200000 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_PhotonCv |
Expert | 0.5 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye2_PhotonBudget |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_Source |
Expert | mEGFP | AF647, AF532, Cy5, ATTO655, ATTO542, Cy3B, mEos3.2, Dendra2, PAmCherry2, mEGFP, mScarlet, DAPI, Hoechst33342, Custom |
The library dye this custom dye starts from. |
Dye3_FluorescentPct |
Expert | 80 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_Qy |
Expert | 0.6 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_ExtCoeff |
Expert | 56000 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_OnSec |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_OffSec |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_BleachProb |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_InitialOnSec |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_Activation405 |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_SpontActivation |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_Primed |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_PrePhotonBudget |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_PhotonCv |
Expert | 0 | A field of this custom dye (a library value until edited; 0 where it does not apply). | |
Dye3_PhotonBudget |
Expert | 100000 | A field of this custom dye (a library value until edited; 0 where it does not apply). |
Renderer¶
How the images are computed: quality, GPU, caches, numerics.
| Property | Tier | Default | Values | Description |
|---|---|---|---|---|
Quality |
Basic | Realistic | Fast, Realistic, Exhaustive, Custom |
Speed vs fidelity: Fast, Realistic (the reference settings) or Exhaustive. Custom: set by hand. |
UseGpu |
Advanced | On | On, Off |
Render on the GPU (Direct3D 11) where a path exists; GpuStatus says which is used. |
GpuStatus |
Advanced (read-only) | Not used yet | What the camera renders on, or why the CPU (read-only). | |
DiskCache |
Advanced | Cells | Off, Cells, CellsAndPsf |
Keep packed cells (and the PSF kernel, ~200 MB) in the per-user cache directory between sessions. |
PsfModel |
Expert | GibsonLanniZernike | Gaussian, RichardsWolf, GibsonLanni, GibsonLanniZernike |
The PSF model (GibsonLanniZernike: scalar Gibson-Lanni + Zernike pupil; RichardsWolf/GibsonLanni: JVM). |
PsfOversampling |
Expert | 6 | 1 .. 16 | PSF kernel samples per camera pixel. |
PsfInterp |
Expert | Cubic | Nearest, Linear, Cubic, Fft |
Sub-pixel placement of the PSF (Fft: exact, slow, CPU only). |
PsfHaloCut |
Expert | 3e-06 | 0 .. 0.001 | Blink splats leave out camera pixels below this share of the emitter's photons (Quality: Fast 1e-5, Realistic 3e-6, Exhaustive 0 = the whole kernel). WideField and other continuous dyes keep the whole kernel. |
PsfPupilSamples |
Expert | 0 | 0 .. 1024 | GibsonLanniZernike pupil samples per axis (0: as many as the kernel window needs; 64: webSMLM's, folds light back into a wide window). |
PsfGeneratorJavaHome |
Expert | JRE/JDK root for the JVM PSF models (empty: auto-detect; read once per process). | ||
WideFieldUpscaling |
Expert | 1 | 1 .. 4 | Mean-field grid cells per pixel (WideField-mode populations). |
WideFieldZPlaneNm |
Expert | 25 | 5 .. 500 | Mean-field dye planes, nm apart. |
BrightFieldQuality |
Expert | 3 | 1 .. 4 | BrightField level 1-4 (sources, samples, slice step unless set below). |
BrightFieldSources |
Expert | 0 | 0 .. 1024 | Condenser source points (0 = the quality's). |
BrightFieldUpscaling |
Expert | 0 | 0 .. 8 | BrightField grid cells per pixel, a minimum (0 = the quality's). |
BrightFieldGeometrySamples |
Expert | 0 | 0 .. 16 | Geometry samples per grid cell (0 = the quality's). |
BrightFieldSliceUm |
Expert | -1 | -1 .. 5 | Multislice step, um (0 = one thin screen, -1 = the quality's). |
MeanFieldDensityPerUm2 |
Expert | 20 | 0 .. 1000000 | Continuous populations denser than this render mean-field. |
MeanFieldSlabNm |
Expert | 500 | 0 .. 10000 | The density's z slab, nm. |
MeanFieldMaxEmitters |
Expert | 5000 | 0 .. 1000000000 | Populations with more emitters than this render mean-field. |
BlinkBinnedDensityPerUm2 |
Expert | 12.5 | 0 .. 1000000000 | A frame's blinks render binned (the same blinks on a sub-pixel grid, FFT-convolved: approximate SMLM, the cost per FOV area instead of per blink) above this many ON emitters per um^2 of the FOV. |
BlinkBinnedMaxEmitters |
Expert | 1000000000 | 0 .. 1000000000 | And binned above this many ON emitters in the frame. |
BlinkBinnedUpscale |
Expert | 2 | 1 .. 8 | Cells of the binned grid per pixel, per axis (a blink is snapped to +-half a cell). |
BlinkMinPhotons |
Expert | 50 | 0 .. 1000000 | A blink with fewer detected photons than this in a frame is not splatted in that frame (Quality: Fast 100, Realistic 50, Exhaustive 0 = every blink); binned and mean-field frames and continuous dyes keep every one. |
BeadClumpsAsOne |
Expert | On | On, Off |
On: a clump of fiducial beads is drawn as one bead of their volume at their centre of mass with their light (faster; Quality Fast, Realistic). Off: each bead of a clump (Exhaustive). |
PatternOnContinuousDyes |
Expert | Off | On, Off |
Under a structured pattern (Lasers.Pattern): On, the blink modes' continuous dyes (dSTORM's initial ON, PALM's pre state) are lit by each frame's pattern (Quality Exhaustive); Off, by the cycle's mean light (Fast, Realistic: ~6x faster live). The blinks and WideField dyes always take the frame's pattern; the kinetics run on the cycle mean either way. |
BlinkMeanFieldDensityPerUm2 |
Expert | 1000000000 | 0 .. 1000000000 | A frame's blinks render mean-field (no blinks drawn: each dye's expected ON time; the blinking itself is lost) above this many expected ON emitters per um^2 of the focal slab. 1e9 = never. |
BlinkMeanFieldMaxEmitters |
Expert | 1000000000 | 0 .. 1000000000 | And mean-field above this many expected ON emitters in the z range. 1e9 = never. |
WriteScopeSpecTo |
Expert | Set to a file path: writes the engine spec of the current settings and stage pose there (insiliscope_cli --spec reproduces the frames). |
For tests only¶
Created only when the process has the environment variable ISC_TEST=1 (the test scripts in tools/), never
by Detail: the precomputed, seeded stack the reproducibility checks use, and tooling hooks.
| Device | Property | Description |
|---|---|---|
Camera |
Test_AcqMode |
|
Camera |
Test_DriftNm |
|
Camera |
Test_EndOfStackReached |
|
Camera |
Test_GenerateStack |
|
Camera |
Test_LivePrefetchMs |
|
Camera |
Test_LiveRenderMs |
|
Camera |
Test_ProfileCollect |
|
Camera |
Test_ProfileWriteTo |
|
Camera |
Test_StackGenerationStatus |
|
Camera |
Test_StackLength |
|
Renderer |
Test_GpuStatus |
GpuStatus at any Detail (read-only). |
Renderer |
Test_WriteRegistryTo |
Set to a file path: writes every row of the property registry there as JSON (the reference docs). |