Inspiration ledger

Whose shoulders SWELL stands on

SWELL invents very little. It combines other people's published work into one box meant to be cheap. Here is who we took from, and what we took. Every entry comes from the sources already cited in the SWELL files, apart from the two differential phase contrast papers, added on 12 October 2026, when that credit was found missing.

Science

  • Fei Chen, Paul Tillberg & Edward Boyden, 2015, Science Expansion microscopy itself: swell the sample, not the optics. Their distortion analysis became SWELL's rule that every gel checks its own expansion. doi:10.1126/science.1260088
  • Paul Tillberg et al., 2016, Nature Biotechnology Protein-retention ExM (proExM) and AcX anchoring: how proteins get tied to the gel. doi:10.1038/nbt.3625
  • Yongxin Zhao et al., 2017, Nature Biotechnology Expansion pathology (ExPath) on clinical specimens: evidence that the chemistry works on real tissue. doi:10.1038/nbt.3892
  • Davide Gambarotto et al., 2019, Nature Methods Ultrastructure ExM (U-ExM): the ~4× heat-and-SDS gel family SWELL starts with. They tuned it with the centriole as a molecular ruler, an early intrinsic ruler. doi:10.1038/s41592-018-0238-1
  • Mikus, Dudin & Dey, "U-ExM of diverse samples", protocols.io, 2025 The starting point for SWELL's wet-lab recipe (not written up yet): monomer mix, stock solutions and timings. doi:10.17504/protocols.io.261gee4qwg47/v1
  • "Neutralising acrylic acid to make sodium acrylate", protocols.io (authors as listed there) The fallback for making sodium acrylate in a lab, in a fume hood only. protocols.io
  • Ons M'Saad & Joerg Bewersdorf, 2020, Nature Communications Pan-ExM and the NHS-ester total-protein stain that gives EM-like contrast. doi:10.1038/s41467-020-17523-8
  • Hugo Damstra et al., 2022, eLife 11:e73775, and its 2022 correction Ten-fold robust ExM (TREx): SWELL's 10× track. The correction taught us to check the TEMED stock concentration. eLife 73775 · correction
  • Yu Shrike Zhang, Jae-Byum Chang et al., 2016, Scientific Reports 6:22691 Expansion mini-microscopy: expansion paired with a webcam mini-microscope, at a hundredth to a thousandth of a benchtop microscope's price. SWELL's first idea, "grow the sample, not the glass", is theirs. doi:10.1038/srep22691
  • Thomas Sheard, Izzy Jayasinghe et al., 2019, ACS Nano 13:2143 Sarcomere periodicity and the fixed width of Z-discs used as intrinsic reporters of local gel expansion, in heart cells. SWELL's muscle ruler is their idea; in our dated searches (docs/design/prior_art.md in the download, 10 October 2026) we found nothing that pairs each myofibril's label-free period before expansion with its own period after. doi:10.1021/acsnano.8b08742
  • Thomas Sheard, 2021, University of Leeds PhD thesis Compared the sarcomere expansion factor with the gel's and found it lower: why this page says a myofibril's expansion may not be the gel's. White Rose eTheses
  • Luca Pesce, Paolo Bianchini et al., 2019, Journal of Biophotonics Nuclear pore complexes as an intrinsic reporter of expansion, from the macro- to the nanoscale. doi:10.1002/jbio.201900018
  • Marisa Vanheusden, Johan Hofkens et al., 2020, ACS Omega Photobleached 3D features as an intrinsic ruler for the expansion factor and for distortions. doi:10.1021/acsomega.0c00118
  • Chozinski et al., 2016, Nature Methods Distortion measured on the same cells before and after expansion: generally below 100 nm (root mean square) over up to 30 µm. doi:10.1038/nmeth.3833
  • Miao, Lin, Qian & Wei, 2022, Journal of Visualized Experiments (VISTA) Label-free images of the same structures before and after expansion, compared to read the expansion factor. SWELL's label-free before-image is not new; we found no use of a widefield, per-fibril period like SWELL's in our dated searches. doi:10.3791/63824
  • Shalin B. Mehta & Colin J. R. Sheppard, 2009, Optics Letters 34(13):1924–1926 Asymmetric illumination-based differential phase contrast (AIDPC): a full-field phase-gradient imaging method, shown on an optical fibre and a histochemically prepared skeletal-muscle section. SWELL's label-free before-image builds on this kind of differential phase contrast. Read from its abstract, 12 October 2026. doi:10.1364/OL.34.001924
  • Lei Tian & Laura Waller, 2015, Optics Express 23(9):11394–11403, and its 2023 erratum Quantitative differential phase contrast in an LED array microscope: phase recovered from pairs of images taken with asymmetric illumination, with several illumination angles for more stable phase recovery. SWELL's four oblique LEDs use this multi-angle, LED-based approach. A 2023 erratum (Optics Express 31(7):11804) corrects typos in the paper's derived transfer functions. Read from the abstracts, 12 October 2026. doi:10.1364/OE.23.011394 · erratum
  • Scheible & Tinnefeld, 2018, bioRxiv preprint DNA-origami nanorulers proposed as measuring references inside the gel. doi:10.1101/265405
  • Hugo Damstra, Lukas Kapitein et al., 2023, Nature Methods (GelMap) A fluorescent grid in the gel that expands with the sample: intrinsic calibration and deformation maps without cellular landmarks. SWELL's whole-gel strain map belongs to this family. doi:10.1038/s41592-023-02001-y
  • Francesca Soglia, Massimiliano Petracci & Eero Puolanne, 2020, Italian Journal of Animal Science Chicken-breast sarcomere lengths by laser diffraction: the reference for the chicken ruler and for the laser experiment. doi:10.1080/1828051X.2020.1761271
  • Collin Douglas et al., 2024, PLoS ONE Z-disc widths of 30–140 nm, depending on the muscle and species: a Z-disc could read out resolution once chicken breast's own Z-disc width is known. doi:10.1371/journal.pone.0300348
  • Migliore, 2022, University of North Texas thesis Prior art: expanded isolated rabbit myofibrils, imaged without labels in transmitted light, with the A-band as the expansion ruler. Muscle can be expanded, and measured from its own structure. UNT Digital Library

Open hardware

  • The OpenFlexure Microscope (Collins et al., 2020, Biomedical Optics Express, and the OpenFlexure community) The 3D-printed flexure stage, optics module and illumination that SWELL planned to fork (v7), plus their advice on which objectives to use. PMC7249832 · build.openflexure.org
  • The Sangaboard (OpenFlexure's motor controller) SWELL's single Pico 2 board was planned to speak the Sangaboard serial protocol, so OpenFlexure habits carry over. openflexure.discourse.group
  • The OpenFlexure forum Plain answers on real stage travel, Pi and camera support, and licensing, which changed SWELL's design. openflexure.discourse.group
  • Raspberry Pi, picamera2 & libcamera The Pi 5 imaging service SWELL planned, with a mono global-shutter camera. raspberrypi.com

Tools and data

  • Python, uv, NumPy, SciPy, Matplotlib Every SWELL simulation and figure. python.org · numpy.org · scipy.org · matplotlib.org · uv
  • MicroscPSF-Py (Gibson–Lanni model), pyotf, rayoptics How sharp a dry objective stays when it focuses into a water gel, and the ray-traced model that was planned but never run. MicroscPSF-Py · pyOTF · ray-optics
  • scikit-image, OpenCV, SimpleITK, elastix, multiview-stitcher Registration and stitching, tested on test images in the toolchain check. scikit-image · OpenCV · SimpleITK · itk-elastix · multiview-stitcher
  • Fiji / ImageJ, QuPath, napari, OME-Zarr Viewing whole gels, and the open data format they would be saved in. fiji.sc · QuPath · napari · OME-NGFF
  • CadQuery, OpenSCAD, FreeCAD, PrusaSlicer The CAD-to-print chain, checked end to end before any part was drawn. CadQuery · OpenSCAD · FreeCAD · PrusaSlicer
  • Pandoc, Typst, Manubot The paper pipeline: references by DOI, numbers straight from data. pandoc.org · typst.app · manubot.org
  • protocols.io, PubMed Central, eLife, FAO AGRIS Open access to the protocols and papers above, which made checking them possible. protocols.io · PMC · eLife · AGRIS
  • three.js (the three.js authors) Draws the 3D concept model at the top of this page. MIT licence. threejs.org
  • Claude (Anthropic), via Claude Code Wrote the audit, simulations, documents and this site. Details in How SWELL was made, below. How SWELL was made

How SWELL was made

Made with AI from a person's brief; not built, and not yet checked by a person

SWELL was designed, simulated and documented with AI (Claude, made by Anthropic), working from the project owner's brief and orders. The AI wrote the audit, the simulation code, the documents, and this website's text and code.

What that means for you

  • simulated Every SWELL result is from simulation until someone builds it. Nothing was measured on a real machine.
  • You can check everything: the download holds the audit, the decisions log, the fact-check table with its sources, the simulation code and its outputs. Rerun the code and compare.
  • An AI can be confidently wrong.

How the work was kept honest

  • Every number from code. Numbers in generated documents are computed from data or a cited source.
  • Every claim tied to a check. A claim must be bound to a passing quality-control metric.
  • Facts with verdicts. Each key fact in the project notes records how far it could be checked against its source (in full, in part, or not yet), with the source (pm/VERIFIED_FACTS.md).
  • Never an author. In any paper, the AI is disclosed as the journal requires and never listed as an author.