Quickstart¶

In the browser: the viewer¶

Nothing to install: the whole simulation runs in your browser as WebAssembly.

It opens in a new tab and loads about 2.5 MB (under 1 MB compressed); a desktop browser with a mouse works best.

A first tour, about five minutes:

Look at the sample. The left half is the sample: an endless field of cells, each with its nucleus, microtubules and nuclear pores. Drag to move the stage, scroll to zoom. Shift-drag tilts and turns the field into 3D; the strip along the bottom is a side view (x-z). View ▾ (top left) switches layers on and off. The dashed square is what the camera sees.
Go live. The live view on the right starts by itself once the engine is up (■ Stop stops it, ▶ Live goes on). Every frame is a simulated camera image of the dashed square: by default DNA-PAINT, so single molecules flash on and off as imagers bind. The sample remembers the light it got, so dyes bleach where you look: move away and back and the place you imaged is dimmer than its fresh neighbours.
Focus and look closer. The Z field (or Page Up / Page Down, or the wheel over the live image) moves the focus through the cells; the side view on the left shows the focal plane. Ctrl + wheel zooms into the live image; Display sets the contrast over a live histogram. On a phone, the live image comes first with the sample as an inset (tap it to swap them); two fingers up or down on the live image focus, a pinch zooms, and the Focus box has a ruler to swipe (the viewer reference has every gesture).
Switch the microscope. In Configuration, Mode changes the experiment: dSTORM, DNA-PAINT, PALM, WideField or BrightField, each with its typical dye, lasers and filters. Try WideField, then BrightField: the same cells, three very different pictures. Drift makes the sample wander, Camera swaps the sCMOS for an EMCCD. Under Illumination & light path each laser is a slider; click the spectra plot for what reaches the camera.
Change the sample. The settings under the image hold the sample and its labels: the microtubules and the nuclear pores each have a mode and a dye (None switches a target off). Specimen mounts DNA-origami Nanorulers instead of cells (set the focus to about 0.02 µm, their dyes lie on the glass), a Bead sample: fiducial beads alone on the glass (focus about 0.05 µm), or a Fluorescent Slide: a uniform dye layer that shows the beam's profile and bleaches where it is brightest. Basic / Advanced / Expert (top right) shows more settings; the search box finds any of them, and every name has a help text on hover (a long press on a phone).
Record a movie. ● Record asks for a number of frames, renders them and plays them back. Save .tif writes a 16-bit TIFF stack that opens in ImageJ/Fiji with its pixel size and frame interval, ready for your SMLM or tracking software. The file's header holds every setting, so insiliscope_cli --spec reproduces it exactly.
Save your setup. The disk icon beside Basic / Advanced / Expert (or Save… in the ☰ menu) writes a .isc.json file in parts (instrument, settings, sample, measurement with the sample's light history, view); the folder icon (Load…) takes all of a file or only some parts, so the same sample can be seen on another microscope.

Everything on the screen, setting by setting: the viewer reference. What the simulation can show, with side-by-side movies: the Gallery.

Micro-Manager¶

The adapter needs a Micro-Manager 2.0 nightly build from 21 February 2026 or later (device interface 75); older builds refuse the DLL.

Download mmgr_dal_inSiliScope.dll and the configurations inSiliScope_Basic.cfg, inSiliScope_Advanced.cfg and inSiliScope_Expert.cfg from the latest release (verify the DLL with its .sha256 file) and copy them into your Micro-Manager folder. The PSF (a scalar Gibson-Lanni model with Zernike aberration modes, or a Gaussian) needs nothing else.
Start Micro-Manager with inSiliScope_Basic.cfg. It loads the hub inSiliScope and one device per part of the microscope: Camera, XYStage, ZStage, Objective, EmissionPath, FilterCube, Lasers, TransmittedLamp, SampleHolder, CellField, Nanorulers, Fiducials, Fluorophores and Renderer, with the config groups
- Channel: one preset per label mode with the cell field's typical dye (AF647 dSTORM, mEos3.2 PALM, ATTO655 DNA-PAINT, mEGFP WideField; the nanorulers' docking strands take their own typical dye in that mode) and BrightField;
- Objective, Camera (Kinetix22 with a 0.667x relay: 97.45 nm pixels at 100x; iXon Ultra 897 with 1.6x: 100 nm), Quality (Fast / Realistic / Exhaustive), Drift (Off / Low / Medium / High / Extreme) and Specimen (CellField / Nanorulers / Beads, the SampleHolder position);
- Illumination (Epi / HILO / TIRF: where the laser spot sits in the objective's back focal plane, Lasers.BfpPosition 0 / 0.95 / 1.03) and BfpPosition (the same as an editable field, 0 = epi, 1 = the critical angle). The channels' light presets set it too: the DNA-PAINT channel HILO, the nanorulers TIRF, the others epi (Illumination geometry); Lasers.Pattern (a property, not a group) makes the light several coherent beams at that radius for structured illumination (SIM2D, SIM3D, the lattices), stepping with every frame an acquisition takes (Structured illumination);
- Laser 561 nm (kW/cm2) and Laser 640 nm (kW/cm2): the two lines' powers at the sample as editable fields in the main window (one property each, Lasers.Laser561KWcm2 / Laser640KWcm2; 0 = off), e.g. 561 alone for the nuclear pores, 640 alone for the microtubules; Quality also sets how much of each blink's PSF halo is drawn: Fast and Realistic leave out pixels below 1e-5 and 3e-6 of the emitter's photons, Exhaustive draws the whole kernel (the halo cut); and which dim blinks are skipped: a blink giving a frame fewer than 100 (Fast) or 50 (Realistic) photons is not drawn in it, Exhaustive draws every one; under a SIM pattern Exhaustive also lights dSTORM's initial-ON and PALM's pre-state dyes with each frame's pattern (Fast and Realistic: the cycle mean, faster);
- and the pixel-size calibration of every objective and camera.

inSiliScope_Advanced.cfg adds the excitation filter, dichroic and emission filter wheels and the channel mEGFP WideField + BrightField; inSiliScope_Expert.cfg shows every property. The hub's pre-init Detail (Basic, Advanced, Expert) decides which properties a session shows; to build a configuration of your own, add the hub inSiliScope in the Hardware Configuration Wizard, then its devices. 3. Take a snapshot of the cell field, move the XY stage, change the Z stage. The Z stage position is the focal plane height above the coverslip (0 = coverslip in focus; it starts at 0.5 um). The Specimen group (or SampleHolder) mounts the DNA-origami nanorulers instead: set the Z stage to about 0.02 um (their dyes lie 13.5 nm above the glass); the Nanorulers device sets their design, density and docking strands per spot (Advanced: the bending's persistence length, the landing). Mounting a sample is a new sample: the lit history and the drift start afresh. Fiducials.DensityPerUm2 (e.g. 0.02) puts fiducial beads on either sample, Fiducials.Type picks the bead. 4. Pick a Channel: the label mode and its typical dye for every target; the lasers and the filter cube follow (Lasers.Preset Auto: the presets of the labelled targets combined). The cell field has two targets, imaged together: the microtubules (CellField.Microtubules_*, ATTO 655 DNA-PAINT at 640 nm) and the nuclear pores (CellField.NuclearPores_*, Cy3B DNA-PAINT at 561 nm, through a multi-band filter set); the nanorulers have one, Nanorulers.Docking_*. Each target has its own mode (_Mode) and label (_Label: Typical, the other dyes with data for that mode, or None to leave it unlabelled); custom dyes are Fluorophores.Dye1..3_* (Expert). In DNA-PAINT, CellField.Microtubules_ImagerNanoMol / Nanorulers.Docking_ImagerNanoMol (Advanced: the imager concentration in the buffer, default 1 nM for the microtubules, 20 nM for the nanorulers) sets how many sites blink per frame: binding events per site per second = k_on × c, from the moment it changes. More imager means denser frames and more free-imager background. 5. The light comes from the shutters: Lasers (fluorescence) and TransmittedLamp (BrightField). With both open (the Utilities Multi Shutter, as in the Advanced channel mEGFP WideField + BrightField) the camera sums the two; with none open it takes dark frames. The autoshutter opens the Core-Shutter for each image.

Every device and property, with its tier and default: Micro-Manager. Snaps, live mode and sequences (also hardware z stacks: the ZStage is sequenceable) render live. Renderer.WriteScopeSpecTo (Expert) writes the settings of the next frame to a file that insiliscope_cli --spec <file> renders. The camera remembers what light each place of the sample has had (snaps, live acquisition and sequences add to it): imaging bleaches and uses up dyes where you imaged, a place never lit starts fresh (dSTORM dyes first in their bright initial ON phase).

The adapter computes the PSF kernel in the background as soon as the device initialises, so the first frame does not wait for it. Renderer.DiskCache (default Cells) keeps the packed cell positions of the field in a small per-user file (%LOCALAPPDATA%\inSiliScope\cache, or $ISC_CACHE_DIR), so a restart with the same seed and cell parameters starts with the cells in place; CellsAndPsf also stores the PSF kernel (one file of ~200 MB at the defaults, read in about half the time it takes to compute); Off writes nothing.

From Python (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", "mEGFP WideField")
core.snapImage(); img = core.getImage()

Command line¶

cmake -S . -B build/native -G Ninja -DCMAKE_BUILD_TYPE=Release
cmake --build build/native --target insiliscope_cli
build/native/cli/insiliscope_cli --out movie.tif --frames 200 --size 128 --seed 42
build/native/cli/insiliscope_cli --specimen Nanorulers --out rulers.tif --frames 1000 --size 64 --exposure-ms 100
build/native/cli/insiliscope_cli --help          # every option and its default
build/native/cli/insiliscope_cli --prepare 1 --disk-cache 2   # warm the caches (world, cells, PSF kernel), no movie
build/native/cli/insiliscope_cli --settings setup.isc.json --out next.tif --frames 100   # the viewer's saved setup
build/native/cli/insiliscope_cli --settings lab.isc.json:instrument --settings mine.isc.json:sample,settings,measurement --out mix.tif

--settings reads a file from the viewer's Save… (all its parts but the view, or those named after a colon; later files and options override). When its measurement holds a light history, the CLI replays it and writes the live sample's next frames, the ones the viewer would take next.

With --drift-xy-speed-nm-per-sec / --drift-z-speed-nm-per-sec the sample drifts (mean speeds; see --help for the direction, its wander and the random-walk jitter --drift-xy-nm-per-sqrt-sec) and the CLI writes the true drift per frame to movie.drift.csv.

The CLI keeps the packed cell positions in the same per-user cache directory as the adapter (--disk-cache 1, the default); --disk-cache 2 adds the PSF kernel, 0 writes nothing.

--specimen Nanorulers mounts the DNA-origami nanorulers (their options --origami-* and the docking strands' label --ruler-*; without --z the focus is on their dyes). The samples and physics pages' figures are made with the CLI's diagnostic outputs, which change no movie: the expected photons before the camera (--photons-out; with --history-before for a sample lit under other settings before the movie, as Micro-Manager's illumination history keeps it), the PSF kernel and pupil (--psf-out), one blink as a movie splats it (--splat-out), the resolved light path and camera (--setup-json), dye sites and schedules (--dyes-json), the mean-field dye density (--density-out), BrightField phase screens (--bf-screens-out) and the preset tables (--presets-json); --help lists them. tools/build_physics_figures.py turns them into the figures.

webSMLM¶

Each release carries cellfield_block.js. In the webSMLM repository run node tools/sync_cellfield.mjs <path to cellfield_block.js>.

Build from source¶

See BUILDING.md in the repository for the build and test steps (core native and WASM, the viewer, the webSMLM block, the Micro-Manager adapter, the docs site).