flowcatchr
A framework for tracking and analyzing flowing blood cells in time lapse microscopy images
Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 16 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A framework for tracking and analyzing flowing blood cells in time lapse microscopy images
Basic Info
- Host: GitHub
- Owner: federicomarini
- License: other
- Language: R
- Default Branch: devel
- Homepage: https://federicomarini.github.io/flowcatchR/
- Size: 23.4 MB
Statistics
- Stars: 4
- Watchers: 2
- Forks: 0
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
flowcatchR
A framework for tracking and analyzing flowing blood cells in time lapse microscopy images
flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides throughout all the steps of bioimage processing, from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations. The main novel contribution investigates the issue of tracking flowing cells such as the ones in blood vessels, to categorize the particles in flowing, rolling and adherent by providing a comprehensive analysis of the identified trajectories. The extracted information is then applied in the study of phenomena such as hemostasis and study of thrombosis development. We expect this package to be potentially applied to a variety of essays, covering a wide range of applications founded on time-lapse microscopy.
Installation
To install the development version for the package flowcatchR, please start a current version of R and type (using devtools):
```r
currently this can be done via github
install.packages("devtools") # if needed devtools::install_github("federicomarini/flowcatchR") ```
If you want to install the current release version, just type:
r
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("flowcatchR")
flowcatchR in a glimpse
r
library("flowcatchR")
data("MesenteriumSubset")
fullResults <- kinematics(trajectories(particles(channel.Frames(MesenteriumSubset,"red"))))
Vignette
To inspect the vignette and the code used in it, type:
```r vignette("flowcatchR-vignette")
and/or
browseVignettes("flowcatchR") ```
Contact
For additional details regarding the functions of flowcatchR, please consult the documentation or write an email to marinif@uni-mainz.de.
Code of Conduct
Please note that the flowcatchR project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Bug reports/Issues/New features
Please use https://github.com/federicomarini/flowcatchR/issues for reporting bugs, issues or for suggesting new features to be implemented.
Owner
- Name: Federico Marini
- Login: federicomarini
- Kind: user
- Location: Mainz
- Company: University Medical Center, Mainz
- Twitter: FedeBioinfo
- Repositories: 173
- Profile: https://github.com/federicomarini
Virchow Fellow, Bioinformatician @ Institute of Medical Biostatistics, Epidemiology and Informatics, Mainz (@imbeimainz)
GitHub Events
Total
- Push event: 7
Last Year
- Push event: 7
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Federico Marini | m****f@u****e | 314 |
| f.marini | f****i@b****8 | 33 |
| Nitesh Turaga | n****a@g****m | 14 |
| Dan Tenenbaum | d****a@f****g | 10 |
| J Wokaty | j****y@s****u | 10 |
| d.tenenbaum | d****m@b****8 | 5 |
| Herve Pages | h****s@f****g | 4 |
| Bioconductor Git-SVN Bridge | b****c@b****g | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****a@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| LiNk-NY | m****9@g****m | 1 |
| j.hester | j****r@b****8 | 1 |
| James Hester | j****r@f****g | 1 |
| Marc Carlson | m****n@f****g | 1 |
| m.carlson | m****n@b****8 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2
- Total pull requests: 0
- Average time to close issues: 10 months
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 2.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
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
Top Authors
Issue Authors
- gilitho (1)
- dmattek (1)
Pull Request Authors
Top Labels
Issue Labels
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Dependencies
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- grimbough/bioc-actions/build-install-check v1 composite
- grimbough/bioc-actions/run-BiocCheck v1 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite
- EBImage * depends
- R >= 2.10 depends
- methods * depends
- BiocParallel * imports
- abind * imports
- colorRamps * imports
- graphics * imports
- plotly * imports
- shiny * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests