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v1.0-doi — Version of record for DOI (identical to v1.0)

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@dabhimanyu dabhimanyu released this 13 Oct 16:01
v1.0-doi
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📦 Release v1.0-doi — Version of record for DOI (identical to v1.0)

Repository: https://github.com/dabhimanyu/bio_math_model_images
Tag: v1.0-doi (byte-for-byte identical to v1.0 at commit d8a945d5a2c2890aeca1e32531badf379d3f2328)
DOI (this version): 10.5281/zenodo.17342495
Concept DOI (all versions): 10.5281/zenodo.17342494

Purpose. Create an immutable, citable Zenodo archive of the exact code used in the Heliyon paper.
Code changes: None. This is the DOI-minted twin of v1.0.

🔗 Associated publication

Makam, A. A.; Dubey, A.; Maharana, S.; Gandasi, N. R.
“Algorithm for semi-automatic detection of insulin granule exocytosis in human pancreatic β-cells.” Heliyon 10 (2024) e38307.
DOI: https://doi.org/10.1016/j.heliyon.2024.e38307

🎯 Scope & Reproducibility

  • Scope: DOI-minted archival snapshot for long-term citation and replication of the paper’s results.
  • Intended use: Run the provided MATLAB pipeline on TIRF stacks for vesicle detection and exocytosis analysis.
  • Stability: This release is frozen for citation; improvements land in subsequent versions.

🧩 Contents (same as v1.0)

  • Pre-processing (edge-preserving filtering; global+local binarization; morphological prep)
  • Vesicle localization (regional maxima + H-max; sub-pixel refinement)
  • Lagrangian tracking; intensity time-traces; undocking vs exocytosis logic
  • Validation on artificial images, TetraSpeck beads, and human β-cell TIRF data

⚙️ System requirements

  • MATLAB: R2022a or newer
  • Toolboxes: Image Processing (required); Parallel Computing (optional, for speedup)
  • GPU: Not required
  • RAM: ≥16 GB recommended for long movies (~10 min @ 30 fps)

🚀 Quick start (this exact snapshot)

git clone https://github.com/dabhimanyu/bio_math_model_images.git
cd bio_math_model_images
git checkout v1.0-doi

In MATLAB:

addpath(genpath(pwd))
if license('test','Distrib_Computing_Toolbox')
    if isempty(gcp('nocreate')), parpool; end
end

📜 Citation

Software (this DOI-minted version):

@software{bio_math_model_images_v1_0_doi,
  author  = {Dubey, Abhimanyu and Makam, Aishwarya A. and Maharana, Shovamayee and Gandasi, Nikhil R.},
  title   = {bio_math_model_images: MATLAB pipeline for vesicle detection and exocytosis analysis},
  url     = {https://github.com/dabhimanyu/bio_math_model_images},
  version = {v1.0-doi},
  year    = {2025},
  doi     = {10.5281/zenodo.17342495},
  note    = {Version of record archived at Zenodo; identical snapshot to v1.0 (commit d8a945d5a2c2890aeca1e32531badf379d3f2328)}
}

Paper:

@article{Makam2024Heliyon,
  author  = {Makam, Aishwarya A. and Dubey, Abhimanyu and Maharana, Shovamayee and Gandasi, Nikhil R.},
  title   = {Algorithm for semi-automatic detection of insulin granule exocytosis in human pancreatic \beta-cells},
  journal = {Heliyon},
  volume  = {10},
  pages   = {e38307},
  year    = {2024},
  doi     = {10.1016/j.heliyon.2024.e38307}
}

🔁 Relationship to v1.0

  • Code parity: 100% (same commit)
  • Reason for new tag: DOI-minted archival record via Zenodo (journal requirement)

📖 Citation & DOI

This repository is archived on Zenodo for long-term citation.
Please cite the concept DOI (stable across all versions) if you wish to refer to the project as a whole.
If citing a specific version (e.g., v1.0-doi), use the version DOI listed on the Zenodo record.

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17342494.svg)](https://doi.org/10.5281/zenodo.17342494)

For the exact DOI of this version (v1.0-doi), see the Zenodo release page or the CITATION.cff file after publication.

How to cite:
Please cite this software as:
Dubey et al. (2025), bio_math_model_images v1.0-doi, Zenodo, 10.5281/zenodo.17342495

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