subprecisioncontactdetection.jl
A Julia package to detect contacts below the precision of a superresolution microscope between 2 subcellular organelles in 2-channel superresolution (STED) microscopy.
https://github.com/bencardoen/subprecisioncontactdetection.jl
Science Score: 77.0%
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 1 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
✓Committers with academic emails
1 of 2 committers (50.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (10.9%) to scientific vocabulary
Keywords
Repository
A Julia package to detect contacts below the precision of a superresolution microscope between 2 subcellular organelles in 2-channel superresolution (STED) microscopy.
Basic Info
Statistics
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 3
- Releases: 0
Topics
Metadata Files
README.md
SubPrecisionContactDetection.jl
Detects sub-precision contacts between subcellular organelles in 2 and 3D STED (precision ~ 50-150nm) superresolution microscopy, for example endoplasmum reticulum and mitochondria (contacts ~ 20-100nm).
Where a pixel precise segmentation is not feasible due to the precision of the microscope, and colocalization does not describe the interface in a meaningful way, SubPrecisionContactDetection can reconstruct the plausible interface between the organelles.
An example rendering of the postprocessed contact zones (white) between endoplasmum reticulum (green) and mitochondria (red) is shown here (source):
Features
- Fast: using multiple threads, and Julia's fast LLVM JIT code
- Reproducible: tests ensure backwards compatibility
- Configurable: Can process deconvolved or raw images, with optional extra denoising
- Rich: provides interpretable features for each detected contact
- Confidence map for each voxel (each voxel has a p-value)
Cite
If you find this project useful, please cite
bibtex
@article{cardoen2023membrane,
title={Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria--ER contacts},
author={Cardoen, Ben and Vandevoorde, Kurt R and Gao, Guang and Ortiz-Silva, Milene and Alan, Parsa and Liu, William and Tiliakou, Ellie and Vogl, A Wayne and Hamarneh, Ghassan and Nabi, Ivan R},
journal={Journal of Cell Biology},
volume={223},
number={1},
pages={e202206109},
year={2023},
publisher={Rockefeller University Press}
}
Owner
- Name: Ben Cardoen
- Login: bencardoen
- Kind: user
- Location: Vancouver
- Company: https://github.com/sfu-mial
- Twitter: BenCardoen
- Repositories: 29
- Profile: https://github.com/bencardoen
PhD Student Computing Science @sfu-mial Simon Fraser University
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Cardoen"
given-names: "Ben"
- family-names: "Vandevoorde"
given-names: "Kurt"
- family-names: "Gao"
given-names: "Guang"
- family-names: "Ortiz-Silva"
given-names: "Milene"
- family-names: "Alan"
given-names: "Parsa"
- family-names: "Liu"
given-names: "William"
- family-names: "Tiliakou"
given-names: "Ellie"
- family-names: "Vogl"
given-names: "A Wayne"
- family-names: "Hamarneh"
given-names: "Ghassan"
- family-names: "Nabi"
given-names: "Ivan Robert"
title: "Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts"
version: 1.0.0
doi: 10.1083/jcb.202206109
date-released: 2024-01-01
url: "https://github.com/github-linguist/linguist"
preferred-citation:
type: article
authors:
- family-names: "Cardoen"
given-names: "Ben"
- family-names: "Vandevoorde"
given-names: "Kurt"
- family-names: "Gao"
given-names: "Guang"
- family-names: "Ortiz-Silva"
given-names: "Milene"
- family-names: "Alan"
given-names: "Parsa"
- family-names: "Liu"
given-names: "William"
- family-names: "Tiliakou"
given-names: "Ellie"
- family-names: "Vogl"
given-names: "A Wayne"
- family-names: "Hamarneh"
given-names: "Ghassan"
- family-names: "Nabi"
given-names: "Ivan Robert"
doi: "10.1083/jcb.202206109"
journal: "Journal Of Cell Biology"
month: 1
start: 1 # First page number
end: 10 # Last page number
title: "Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts"
issue: 1
volume: 1
year: 2024
GitHub Events
Total
- Create event: 6
- Release event: 1
- Issues event: 4
- Issue comment event: 2
- Push event: 130
Last Year
- Create event: 6
- Release event: 1
- Issues event: 4
- Issue comment event: 2
- Push event: 130
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ben Cardoen | 2****n | 229 |
| Ben Cardoen | b****n@d****a | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 6
- Total pull requests: 0
- Average time to close issues: 18 days
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.33
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 0
- Average time to close issues: 18 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.33
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- bencardoen (6)