Science Score: 23.0%
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
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○Scientific vocabulary similarity
Low similarity (14.2%) to scientific vocabulary
Keywords
Repository
R package for deep learning image segmentation
Basic Info
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- Stars: 20
- Watchers: 1
- Forks: 2
- Open Issues: 0
- Releases: 1
Topics
Metadata Files
README.md
imageseg
R package for deep learning image segmentation using the U-Net model architecture by Ronneberger (2015), implemented in Keras and TensorFlow. It provides pre-trained models for forest structural metrics (canopy density and understory vegetation density) and a workflow to apply these on custom images.
In addition, it provides a workflow for easily creating model input and model architectures for general-purpose image segmentation based on the U-net architecture. Model can be trained on grayscale or color images, and can provide binary or multi-class image segmentation as output.
The package can be found on CRAN:
https://cran.r-project.org/web/packages/imageseg/index.html
The preprint of the paper describing the package is available on bioRxiv:
https://doi.org/10.1101/2021.12.16.469125
Installation
First, install the R package "R.rsp" which enables the static vignettes.
r
install.packages(R.rsp)
Install the imageseg package from CRAN via:
r
install.packages(imageseg)
Alternatively you can install from GitHub (requires remotes package and R.rsp):
r
library(remotes)
install_github("EcoDynIZW/imageseg", build_vignettes = TRUE)
Using imageseg requires Keras and TensorFlow. See the vignette for information about installation and initial setup:
Tutorial
See the vignette for an introduction and tutorial to imageseg.
r
browseVignettes("imageseg")
The vignette covers:
- Installation and setup
- Sample workflow for canopy density assessments
- Training new models
- Continued training of existing models
- Multi-class image segmentation models
- Image segmentation based on grayscale images
Forest structure model download
The models, example predictions, training data and R script for model training for both the canopy and understory model are available from Dryad as a single download:
https://doi.org/10.5061/dryad.x0k6djhnj
See the "Usage Notes" section for details on the dataset.
The models and script (without the training data) are also hosted on Zenodo and can be downloaded individually from:
https://doi.org/10.5281/zenodo.6861157
The pre-trained models for forest canopy density and understory vegetation density are available for download. The zip files contain the model (as .hdf5 files) and example classifications to give an impression of model performance and output:
Canopy model: https://zenodo.org/record/6861157/files/imagesegcanopymodel.zip?download=1
Understory model: https://zenodo.org/record/6861157/files/imagesegunderstorymodel.zip?download=1
Please see the vignette for further information on how to use these models.
Training data download
Training data for both the canopy and understory model are included in the Dryad dataset download in the zip files:
imagesegcanopytraining_data.zip
imagesegunderstorytraining_data.zip
For details, please see the Usage Notes and the info.txt files contained in the zip files.
The training data are not required for users who only wish to use the pre-trained models on their own images.
Owner
- Name: Ecological Dynamics Department
- Login: EcoDynIZW
- Kind: organization
- Location: Berlin
- Website: https://ecodynizw.github.io/
- Twitter: EcoDynIZW
- Repositories: 14
- Profile: https://github.com/EcoDynIZW
We are scientists of the Department of Ecological Dynamics at the Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
GitHub Events
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- Issues event: 2
- Watch event: 1
Last Year
- Issues event: 2
- Watch event: 1
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jürgen Niedballa | c****r@g****m | 48 |
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Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 1
- Average time to close issues: 2 months
- Average time to close pull requests: 4 months
- Total issue authors: 5
- Total pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: 9 minutes
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
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- jniedballa (1)
- williamhoole (1)
- bappa10085 (1)
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- williamhoole (1)
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Packages
- Total packages: 1
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Total downloads:
- cran 231 last-month
- Total docker downloads: 11
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
cran.r-project.org: imageseg
Deep Learning Models for Image Segmentation
- Documentation: http://cran.r-project.org/web/packages/imageseg/imageseg.pdf
- License: MIT + file LICENSE
-
Latest release: 0.5.0
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- doParallel * imports
- dplyr * imports
- foreach * imports
- grDevices * imports
- keras * imports
- magick * imports
- magrittr * imports
- methods * imports
- parallel * imports
- purrr * imports
- stats * imports
- tibble * imports
- R.rsp * suggests
- testthat * suggests