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v0.13.0 — Physically modelled simulator, Compare to GT & MLE shape test

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@jhohlbein jhohlbein released this 01 Oct 18:41
· 40 commits to main since this release
v0.13.0
5d7190f

Full details in CHANGELOG.md.

Highlights

  • A physically modelled simulator with a known answer (Simulate movie). A labelled 3D structure — microtubule networks in whole cells (the inSiliScope world model, compiled to WebAssembly), nuclear pore complexes, filaments, a tilted plane, a uniform volume or a spherical shell — with blinking and bleaching molecules, a structured background, an sCMOS or EMCCD camera and a vectorial Gibson-Lanni PSF with Zernike aberrations (astigmatism, coma, extended-depth presets). Seeded runs are exactly reproducible; frames render on the GPU when available. Show movie, Save sim. movie (16-bit TIFF + ground-truth CSV) and Save/Load ground truth keep a simulation reusable; Calib. 3D stack simulates a matching bead stack.
  • Compare to GT scores a Localize result against the simulation's ground truth: detection, lateral and axial error (median and percentiles), per molecule and per depth, photometry, and measured precision against both the fit's own CRLB and the theoretical CRLB of the true emitters — also for phasor. A step-by-step Simulation guide with worked recipes is in the documentation.
  • MLE shape test (after Smith et al., Nat. Methods 2010): every MLE fit reports its mean per-pixel log-likelihood ratio (llr, also a CSV and table column) and fits scoring below −1 are dropped — mostly windows with a second emitter in reach. On by default for the MLE methods; switch it off for aberrated PSFs. Identical on CPU, worker pool and GPU.
  • Interface: refusals, failures and warnings in the log start with a bold red !!! and say what to do; the Simulation section sits below 3D calibration (Alt+Shift hotkeys follow); View/Hide ground truth and small panel resizes keep the reconstruction's zoom.

Credits. The simulator and Compare to GT come from PR #10 by Koen J. A. Martens (Zernike-aberrated PSF and 3D simulation, structure library, the inSiliScope cell field — BSD-3-Clause, licence text in the page source — and the nuclear-pore-complex model) and Carlas Smith (photophysics, background, illumination, EMCCD camera, test structures, engineered PSFs, ground-truth scoring).

Archived on Zenodo with its own version DOI — the concept DOI 10.5281/zenodo.21445041 always resolves to the latest.

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