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MicroTracker.jl

MicroTracker.jl: A Julia package for microbot research - Published in JOSS (2024)

https://github.com/czimm79/microtracker.jl

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 11 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: nature.com, joss.theoj.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Engineering Computer Science - 40% confidence
Last synced: 6 months ago · JSON representation ·

Repository

Microbot tracking and analysis with Julia.

Basic Info
  • Host: GitHub
  • Owner: czimm79
  • License: mit
  • Language: Julia
  • Default Branch: master
  • Homepage:
  • Size: 548 MB
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 9
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

MicroTracker.jl

Docs Coverage DOI

MicroTracker.jl is a feature-complete Julia package that tracks and analyzes moving microbots in microscopy video. This package tracks critical microbot metrics including size, velocity, and rotation rate. Combined with easy batch processing of videos, MicroTracker enables high-throughput analysis across multiple global experimental variables. For more information on microbots and this package, please see the short paper.

https://github.com/czimm79/MicroTracker.jl/assets/49537407/12c9a035-8b00-4576-a21b-ec7b8fa87629

To get started, view the docs by clicking the Docs badge and click Quick Start on the left side. This package is designed for users with limited coding or Julia experience. Please raise an issue or start a pull request if anything could be improved.

Collaboration/Contributing

MicroTracker is built for collaboration and use across the microbot research field. To get started contributing and improving the package, see the setup guide. To report an issue, use the Issues tab 👆. Lastly, to seek support or discuss MicroTracker, please use the Discussions tab.

Extra information

Various components of MicroTracker have been used in scholarly works[^1][^2][^3][^4]. This package open sources, combines, and tests the tools written for microbot tracking as part of Coy Zimmermann's PhD thesis work 2018-2023 on magnetically propelled microwheels. This work was performed in the Marr Group at the Colorado School of Mines and with collaboration of the Neeves Lab at the University of Colorado Denver, Anschutz Medical Campus. MicroTracker uses and builds on work from colloidal science researchers[^5][^6].

[^1]: E. Wolvington, L. Yeager, Y. Gao, C. J. Zimmermann, and D. W. M. Marr, “Paddlebots: Translation of Rotating Colloidal Assemblies near an Air/Water Interface,” Langmuir, vol. 39, no. 22, pp. 7846–7851, Jun. 2023, doi: 10.1021/acs.langmuir.3c00701. [^2]: M. J. Osmond, E. Korthals, C. J. Zimmermann, E. J. Roth, D. W. M. Marr, and K. B. Neeves, “Magnetically Powered Chitosan Milliwheels for Rapid Translation, Barrier Function Rescue, and Delivery of Therapeutic Proteins to the Inflamed Gut Epithelium,” ACS Omega, vol. 8, no. 12, pp. 11614–11622, Mar. 2023, doi: 10.1021/acsomega.3c00886. [^3]: C. J. Zimmermann, P. S. Herson, K. B. Neeves, and D. W. M. Marr, “Multimodal microwheel swarms for targeting in three-dimensional networks,” Sci Rep, vol. 12, no. 1, p. 5078, Dec. 2022, doi: 10.1038/s41598-022-09177-x. [^4]: C. J. Zimmermann, T. Schraeder, B. Reynolds, E. M. DeBoer, K. B. Neeves, and D. W. M. Marr, “Delivery and actuation of aerosolized microbots,” Nano Select, p. nano.202100353, Mar. 2022, doi: 10.1002/nano.202100353. [^5]: J. C. Crocker and D. G. Grier, “Methods of Digital Video Microscopy for Colloidal Studies,” Journal of Colloid and Interface Science, vol. 179, no. 1, pp. 298–310, Apr. 1996, doi: 10.1006/jcis.1996.0217. [^6]: D. B. Allan, T. Caswell, N. C. Keim, C. M. van der Wel, and R. W. Verweij, “soft-matter/trackpy: v0.6.1.” Zenodo, Feb. 2023. doi: 10.5281/zenodo.7670439.

Owner

  • Name: Coy Zimmermann
  • Login: czimm79
  • Kind: user
  • Location: Golden, CO
  • Company: Colorado School of Mines

👋 I am a PhD Chemical Engineer researching microbots for biomedical applications. I use Julia and Python for high-throughput data analysis and modeling.

JOSS Publication

MicroTracker.jl: A Julia package for microbot research
Published
February 13, 2024
DOI
Volume 9, Issue 94, Page 5804
Authors
Coy J. Zimmermann
Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, United States of America
Keith B. Neeves
Departments of Bioengineering and Pediatrics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, United States of America
David W.m. Marr
Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, United States of America
Editor
Kevin M. Moerman ORCID
Tags
microbot tracking colloids microrobotics biomedical
View PDF Review Thread Software Archive

Citation (citation.cff) 

cff-version: "1.2.0"
authors:
- family-names: Zimmermann
  given-names: Coy J.
- family-names: Neeves
  given-names: Keith B.
- family-names: Marr
  given-names: David W. M.
doi: 10.5281/zenodo.10578580
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Zimmermann
    given-names: Coy J.
  - family-names: Neeves
    given-names: Keith B.
  - family-names: Marr
    given-names: David W. M.
  date-published: 2024-02-13
  doi: 10.21105/joss.05804
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5804
  title: "MicroTracker.jl: A Julia package for microbot research"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05804"
  volume: 9
title: "MicroTracker.jl: A Julia package for microbot research"

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 152
  • Total Committers: 2
  • Avg Commits per committer: 76.0
  • Development Distribution Score (DDS): 0.066
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Coy Zimmermann c****9@g****m 142
CompatHelper Julia c****y@j****g 10
Committer Domains (Top 20 + Academic)
julialang.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 47
  • Average time to close issues: 2 months
  • Average time to close pull requests: 13 days
  • Total issue authors: 4
  • Total pull request authors: 2
  • Average comments per issue: 1.63
  • Average comments per pull request: 0.83
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 17
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • BioTurboNick (5)
  • Kevin-Mattheus-Moerman (1)
  • czimm79 (1)
  • JuliaTagBot (1)
Pull Request Authors
  • czimm79 (34)
  • github-actions[bot] (16)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 8
juliahub.com: MicroTracker

Microbot tracking and analysis with Julia.

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 9.8%
Dependent packages count: 38.1%
Average: 44.3%
Forks count: 54.4%
Stargazers count: 74.9%
Last synced: 6 months ago

Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v2 composite
  • codecov/codecov-action v2 composite
  • julia-actions/cache v1 composite
  • julia-actions/julia-buildpkg v1 composite
  • julia-actions/julia-docdeploy v1 composite
  • julia-actions/julia-processcoverage v1 composite
  • julia-actions/julia-runtest v1 composite
  • julia-actions/setup-julia v1 composite
.github/workflows/TagBot.yml actions
  • JuliaRegistries/TagBot v1 composite
.github/workflows/CompatHelper.yml actions
.github/workflows/draft-pdf.yml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v1 composite
  • openjournals/openjournals-draft-action master composite
paper/environment.yml pypi