Inspiration ledger灵感账本

Whose shoulders SWELL stands onSWELL 站在谁的肩膀上

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.

SWELL 自己发明的东西很少，它是把别人已经发表的成果拼进一个以低成本为目标的盒子里。下面列出我们向谁借了什么。每一条都来自 SWELL 文件里已经引用过的出处。

Science科学

  • 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. 膨胀显微技术本身：放大样品，而不是放大光学系统。他们的形变分析，成了 SWELL"每块凝胶自己检验膨胀"的规矩。 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. 蛋白保留型 ExM（proExM）和 AcX 锚定：蛋白质怎样被拴在凝胶上。 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. 临床标本上的膨胀病理（ExPath）：证明这套化学在真实组织上行得通。 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. 超微结构 ExM（U-ExM）：SWELL 起步用的约 4 倍、加热加 SDS 变性的凝胶体系。他们用中心粒当分子标尺来调这套方法，这是较早的内在标尺。 doi:10.1038/s41592-018-0238-1
  • Mikus, Dudin & Dey, "U-ExM of diverse samples", protocols.io, 2025 The v0 wet-lab recipe: monomer mix, stock solutions and timings. v0 湿实验配方：单体混合液、母液和时间安排。 doi:10.17504/protocols.io.261gee4qwg47/v1
  • "Neutralising acrylic acid to make sodium acrylate", protocols.io (authors as listed there)"Neutralising acrylic acid to make sodium acrylate"，protocols.io（作者见原页面） The fallback for making sodium acrylate in a lab, in a fume hood only. 在实验室里自制丙烯酸钠的备用方案（只能在通风橱里做）。 protocols.io
  • Ons M'Saad & Joerg Bewersdorf, 2020, Nature Communications Pan-ExM and the NHS-ester total-protein stain that gives EM-like contrast. Pan-ExM 和 NHS 酯全蛋白染色，带来类似电镜的反差。 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. 十倍稳健 ExM（TREx）：SWELL 的 10 倍路线。那份更正让我们学会核对 TEMED 母液浓度。 eLife 73775 · correction更正
  • 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. 膨胀迷你显微：把膨胀显微和网络摄像头迷你显微镜配在一起，价格只有台式显微镜的百分之一到千分之一。SWELL 的第一个想法"放大样本，而不是升级镜头"，是他们先提出的。 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; SWELL adds the paired, label-free before-image of each myofibril. 在心肌细胞里，用肌节周期和 Z 盘的固定宽度作为凝胶局部膨胀的内在指示。SWELL 的肌肉标尺是他们的想法；SWELL 加的是每根肌原纤维膨胀前的免标记配对图像。 doi:10.1021/acsnano.8b08742
  • Thomas Sheard, 2021, University of Leeds PhD thesis利兹大学博士学位论文 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. 把肌节算出的膨胀倍数和凝胶的比较，发现前者更低：所以本页说，肌原纤维的膨胀不一定等于凝胶的膨胀。 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. 用核孔复合体作为膨胀的内在指示，从宏观尺度一直到纳米尺度。 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. 用光漂白出的三维图案作为内在标尺，量膨胀倍数和形变。 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. 在同一批细胞的膨胀前后测量形变：在 30 µm 以内的尺度上，均方根形变一般低于 100 nm。 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; its cheap, widefield, per-fibril period is the difference. 比较同一结构膨胀前后的免标记图像来读出膨胀倍数。SWELL 的免标记膨胀前图像并不新；不同之处在于它用便宜的宽场显微、逐根纤维地读周期。 doi:10.3791/63824
  • Scheible & Tinnefeld, 2018, bioRxiv preprintbioRxiv 预印本 DNA-origami nanorulers proposed as measuring references inside the gel. 提出把 DNA 折纸纳米尺放进凝胶里，当作测量参照。 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. 在凝胶里放一张荧光网格，随样品一起膨胀：不靠细胞结构就能校准倍数、画出形变图。SWELL 的整块凝胶应变图属于这一类方法。 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. 用激光衍射测的鸡胸肉肌节长度：鸡肉标尺和激光小实验的参考值。 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. Z 盘宽 30–140 纳米，因肌肉和物种而异：等鸡胸肉自己的 Z 盘宽度知道了，Z 盘才能用来读出分辨率。 doi:10.1371/journal.pone.0300348
  • Migliore, 2022, University of North Texas thesis北德克萨斯大学学位论文 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. 现有工作：膨胀分离的兔肌原纤维，用透射光不染色成像，并以 A 带作为膨胀的尺子。肌肉可以膨胀，也能用它自己的结构来量。 UNT Digital Library

Open hardware开源硬件

  • The OpenFlexure Microscope (Collins et al., 2020, Biomedical Optics Express, and the OpenFlexure community)OpenFlexure 显微镜（Collins 等，2020，Biomedical Optics Express，以及 OpenFlexure 社区） The 3D-printed flexure stage, optics module and illumination that SWELL planned to fork (v7), plus their advice on which objectives to use. 3D 打印的柔性载物台、光学模块和照明，SWELL 原计划直接衍生（v7）；还有他们关于物镜选择的建议。 PMC7249832 · build.openflexure.org
  • The Sangaboard (OpenFlexure's motor controller)Sangaboard（OpenFlexure 的电机控制板） SWELL's single Pico 2 board was designed to speak the Sangaboard serial protocol, so OpenFlexure habits carry over. SWELL 那块 Pico 2 控制板被设计成兼容 Sangaboard 的串口协议，OpenFlexure 的用法可以直接沿用。 openflexure.discourse.group
  • The OpenFlexure forumOpenFlexure 论坛 Plain answers on real stage travel, Pi and camera support, and licensing, which changed SWELL's design. 关于载物台实际行程、Pi 和相机支持、许可证的直接回答，这些都改变了 SWELL 的设计。 openflexure.discourse.group
  • Raspberry Pi, picamera2 & libcamera The Pi 5 imaging service SWELL planned, with a mono global-shutter camera. SWELL 计划用的 Pi 5 成像服务，配一台黑白全局快门相机。 raspberrypi.com

Tools and data工具与数据

  • Python, uv, NumPy, SciPy, Matplotlib Every SWELL simulation and figure. SWELL 的每一个仿真和每一张图。 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. 干物镜对焦进水凝胶时还能保持多清晰，以及原计划要做、但没做成的光线追迹模型。 MicroscPSF-Py · pyOTF · ray-optics
  • scikit-image, OpenCV, SimpleITK, elastix, multiview-stitcher Registration and stitching, tested on test images in the toolchain check. 配准和拼接，已在工具链自检里用测试图像测试过。 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. 查看整块凝胶的图像，以及保存它们的开放数据格式。 fiji.sc · QuPath · napari · OME-NGFF
  • CadQuery, OpenSCAD, FreeCAD, PrusaSlicer The CAD-to-print chain, checked end to end before any part was drawn. 从 CAD 到打印的整条工具链，在画任何零件之前就已整体打通验证。 CadQuery · OpenSCAD · FreeCAD · PrusaSlicer
  • Pandoc, Typst, Manubot The paper pipeline: references by DOI, numbers straight from data. 论文流水线：按 DOI 引用文献，数字直接取自数据。 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. 上面这些实验方案和论文的开放获取渠道，让核查成为可能。 protocols.io · PMC · eLife · AGRIS
  • three.js (the three.js authors) Draws the 3D concept model at the top of this page. MIT licence. 页面顶部的 3D 概念模型就是用它画的。MIT 许可。 threejs.org
  • Claude (Anthropic), via Claude Code Wrote the audit, simulations, documents and this site. Details in AI transparency below. 写了审计、仿真、文档和这个网站。详见下面的 AI 透明度。 AI transparencyAI 透明度

AI transparencyAI 透明度

Made by an AI, from a person's brief. Built by nobody, yet.AI 做的，按一个人的要求做。还没人造出来。

SWELL was designed, simulated and documented by an AI: Claude, made by Anthropic, used through Claude Code, working from the project owner's brief and orders. The project stopped before its first gate (G0). The AI wrote the audit, the simulation code, the documents, and this website's text and code.

SWELL 的设计、仿真和文档都是由 AI 完成的：用的是 Anthropic 公司的 Claude，通过 Claude Code 使用，依据项目负责人的任务书和指令来做。项目在第一道关卡（G0）之前就停了。审计、仿真代码、文档，以及这个网站的文字和代码，都是 AI 写的。

What that means for you这对你意味着什么

  • 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.
  • 模拟 在有人真正造出来之前，SWELL 的每一个结果都来自仿真。没有任何数据是在真机上测的。
  • 一切都能查：下载包里有审计报告、决策日志、带出处的事实核查表、仿真代码和输出结果。重新跑一遍代码，对照一下。
  • AI 也会一本正经地出错。

How the AI was kept honest怎么让 AI 保持诚实

  • Every number from code. Numbers in generated documents are computed from data or a cited source (invariant INV-18).
  • Every claim tied to a check. A claim must be bound to a passing QC metric (INV-15).
  • A second pair of eyes. Work counts as checked only after a fresh AI session that didn't build it has checked it. That is an AI check, not a person's.
  • Facts with verdicts. Each key fact in the project notes records how far an AI could check it 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.
  • 每个数字都来自代码。生成文档里的数字都由数据或有出处的来源计算得出（不变量 INV-18）。
  • 每个结论都绑定检验。结论必须对应一项通过的质控指标（INV-15）。
  • 第二双眼睛。一项工作只有经过一个没参与制作的新 AI 会话检查，才算“检查过”。这是 AI 的检查，不是人的。
  • 事实带判定。项目笔记里的每条关键事实，都记下 AI 对照出处能核对到什么程度（全部、部分或尚未），并附出处（pm/VERIFIED_FACTS.md）。
  • 从不署名。任何论文里，AI 都会按期刊要求如实披露，但绝不列为作者。