inSiliScope
A deterministic in-silico microscope. inSiliScope generates an endless field of synthetic cells (cell body,
nucleus, cytoplasm, microtubules, nuclear pores, dye sites) -- or a field of DNA-origami nanorulers -- and images it as a
single-molecule localisation (SMLM) movie or as a widefield image, with a physical PSF and camera noise model. Every
cell and molecule is a pure function of (seed, address), so any window of the field can be generated on its own, in
any order, on any platform, with identical results.
| A field of synthetic cells | What is in the box | Widefield camera | Single-molecule (SMLM) camera |
|---|
| | | |
- Live viewer (browser, WebAssembly): pan, tilt and turn through the field in 3D, look through a live microscope
(the adapter's live mode with the sample's illumination history, set up with its Micro-Manager config presets) and
record TIFF stacks; make animations of a cell (orbits, layers building up, slices sweeping through) and export them
as MP4, WebM or GIF.
- Micro-Manager adapter: a hub with one device per part of the microscope (camera, stages, objective, filters, lasers, lamp, sample, labels, renderer) at three levels of detail, and ready-made configurations; live acquisitions against a sample that never changes.
- webSMLM block: the same core as one generated JS file.
The viewer (live in your browser): https://kjamartens.github.io/inSiliScope/ -- docs, gallery and benchmarks: https://kjamartens.github.io/inSiliScope/docs/
Get it
| I want to... | Do this |
|---|
| try it | open the viewer (a quick tour) |
| use it in Micro-Manager | install a Micro-Manager 2.0 nightly build (21 February 2026 or later: device interface 75), download mmgr_dal_inSiliScope.dll and inSiliScope_Basic.cfg from the latest release, copy them to your Micro-Manager folder (Windows x64) and load the configuration (getting started) |
| script it | build insiliscope_cli (below) and write TIFF movies headlessly |
What it models
- Samples: the cell field or DNA-origami nanorulers (200 x 13 nm rods with three spots of docking strands 80 nm
apart, bent in the coverslip plane as a worm-like chain), switched in the viewer, Micro-Manager's
SampleHolder or the
CLI's --specimen (Samples); optional fiducial beads on
either (gold, TetraSpeck, FluoSpheres, nanodiamonds; spectra and brightness after Balinovic et al. 2019; on the
coverslip, on the sample or in a gel; slow bleaching), for drift correction
(Fiducial beads), or alone (the bead sample); a
fluorescent slide, a uniform dye layer that bleaches where the beam is brightest
(Fluorescent slide).
- Cell field: jittered-grid cell placement with relaxation packing, wobbly cell outlines, a shaped 3D nucleus, a cytoplasm height
field, 3D microtubules from the nucleus to the cell edge, a 13_3 protofilament dye lattice, nuclear pore complexes
(Nup96, 64 sites) over the whole nuclear envelope; each target labelled on its own (two colours at once by default)
through a probe model (antibodies, nanobody, SNAP/Halo, ...: binder, flexibility, linker).
- Labels, dyes, light path: a dye library (FPbase spectra, literature kinetics) in four label modes -- dSTORM
(initial ON, blinking, intensity-scaled times), PALM (pre-converted state, 405 nm and primed activation), DNA-PAINT
(imager binding, free-imager background) and WideField (all dyes at once, bleaching by photon budget); lasers,
dichroics, emission filters and camera QE curves set excitation, detected fraction and each state's PSF wavelength
(Dyes and light path).
- Fluorescence imaging: blinks splatted with a diffraction PSF (a scalar Gibson-Lanni model with Zernike
aberration modes, double helix) or a Gaussian, continuous populations mean-field (3D PSF
convolution by FFT, GPU path: WebGPU / Direct3D 11) or per dye, sub-pixel placement, sCMOS/EMCCD noise, background,
drift, hardware z stacks; the light as a spot in the back focal plane (epi / HILO / TIRF) or several coherent beams
(2D, 3D and lattice SIM, phase-stepped with the frame).
- BrightField (exploration): transmitted light through the cells' refractive index (cytoplasm, nucleus,
microtubules only -- nothing the world does not simulate), partially coherent Koehler illumination, multislice
wave optics, one quality setting from fast to precise ().
Documentation of the models: Samples and
Physics. The algorithm notes (the why of each design decision) are in spec/ALGORITHM.md.
Build
# core + CLI, native (Linux/macOS)
cmake -S . -B build/native -G Ninja -DCMAKE_BUILD_TYPE=Release
cmake --build build/native
ctest --test-dir build/native -j 8
build/native/cli/insiliscope_cli --out movie.tif --frames 200 --size 128 # --help for all options
# Windows (MSVC)
cmake --preset msvc && cmake --build --preset msvc && ctest --test-dir build/msvc -C Release -j 8
# WASM (Emscripten 6.0.10) and the viewer module
cmake --preset wasm && cmake --build --preset wasm && node tools/embed_web_module.mjs
The Micro-Manager adapter is MSBuild-only and needs the third_party/mmCoreAndDevices submodule and a locally built
third_party/SMLMPsfEmbedded.jar; see BUILDING.md.
Tagged releases build everything in CI (.github/workflows/release.yml).
Repository layout
core/ world model, C++17, no MMDevice/GPU/OS deps; C ABI in core/include/insiliscope/
adapter/inSiliScope/ the Micro-Manager device adapter (MSBuild) and Simulation/, the render engine
cli/ insiliscope_cli (headless TIFF movies) and the viewer's WASM target
web/ the viewer (the WASM core and engine)
spec/ algorithm notes, port spec, frozen golden vectors
tests/ tools/ parity and golden harness, GPU checks, adapter smoke tests, release tooling
docs/ gallery/ the project site (mkdocs) and the manifest rendered into the gallery
Contributing
See CONTRIBUTING.md and docs/extending.md. Ideas: docs/roadmap.md.
Citing
See CITATION.cff.
License
This project's source is BSD-3-Clause (LICENSE). The distributed Micro-Manager DLL is GPL-3.0
(LICENSE-GPL-3.0.txt). The viewer and the webSMLM block are BSD-3-Clause. Third-party components and credits:
THIRD_PARTY_NOTICES.md. inSiliScope builds on
webSMLM (MIT) and its camera and PSF models.
