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Citations and Acknowledgements

Use this list for methods supplements, license review, and dataset attribution.

Cite MorphoStack (required shoutout)

If you use MorphoStack in research, teaching, benchmarks, products, or derivative tools, please:

  1. Cite the software using CITATION.cff (GitHub “Cite this repository”).
  2. Name MorphoStack in papers, READMEs, or product docs where practical.
  3. Keep license notices when you redistribute code (see LICENSE).

Suggested citation:

Abhinav. MorphoStack: local morphometry toolkit for microscopy Z-stacks (v0.1.0). 2026.
https://github.com/sudoax0n/MorphoStack

BibTeX-style:

@software{morphostack2026,
  author  = {Abhinav},
  title   = {MorphoStack: local morphometry toolkit for microscopy Z-stacks},
  version = {0.1.0},
  year    = {2026},
  url     = {https://github.com/sudoax0n/MorphoStack}
}

MorphoStack license (dual)

Option SPDX Use when
GNU AGPL v3 only AGPL-3.0-only You can comply with copyleft / network source disclosure
PolyForm Noncommercial 1.0.0 PolyForm-Noncommercial-1.0.0 Noncommercial research, education, personal use

Commercial closed-source use: contact the author (see LICENSE).

Full texts:

Third-party JavaScript loaded at runtime in standalone mesh HTML exports (e.g. Plotly CDN) remains under the respective library licenses.

Core libraries

Component Role in MorphoStack Suggested citation / reference
NumPy Arrays and numerics Harris et al., Nature 585, 357–362 (2020)
SciPy Morphology, marching cubes helpers Virtanen et al., Nature Methods 17, 261–272 (2020)
scikit-image Segmentation helpers, marching cubes van der Walt et al., PeerJ 2:e453 (2014)
OpenCV Contours and morphology Bradski, Dr. Dobb's Journal (2000)
Plotly Browser 3D mesh preview Plotly Technologies Inc.
tifffile / czifile Stack I/O Library docs / format specs
Shapely Polygon utilities shapely.readthedocs.io
FastAPI / Uvicorn Local API server fastapi.tiangolo.com

Methods notes

  • Threshold + connected components — standard image-processing practice; MorphoStack’s implementation is original but follows common Fiji/ImageJ and OpenCV workflows.
  • Active surfaces — in-house experimental surfel refinement. Describe as experimental in methods text; not a third-party plugin port.

Reference datasets

  • DOPC Movie 1 (syst202400052-sup-0001-movie1-dopc.tif) — supplementary data associated with Shape Analysis of Biomimetic and Plasma Membrane Vesicles (DOI 10.1002/syst.202400052). Cite the original paper when using this dataset in figures or validation tables.

Related

methods.md · validation.md · ../LICENSE