https://github.com/wpbonelli/herbarium-sheets
trait analysis for digitized herbarium sheets
https://github.com/wpbonelli/herbarium-sheets
Last synced: 8 months ago
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trait analysis for digitized herbarium sheets
- Host: GitHub
- URL: https://github.com/wpbonelli/herbarium-sheets
- Owner: wpbonelli
- Created: 2021-08-02T18:26:32.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2021-08-07T21:29:57.000Z (almost 5 years ago)
- Last Synced: 2025-05-05T01:09:02.017Z (about 1 year ago)
- Language: Python
- Homepage:
- Size: 96.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Herbarium Sheets
Extract geometric trait measurements from scans or images of herbarium sheets.
## Acknowledgements
General approach inspired by Suxing Liu, in particular [Smart Plant Growth Top-Down Traits](https://github.com/Computational-Plant-Science/spg).
[PlantCV](https://github.com/danforthcenter/plantcv) also used for skeletonization, pruning, leaf & stem counting, etc.
## Requirements
[Docker](https://www.docker.com/) is required to run this project in a Unix environment.
## Installation
To install from source, clone the project with `git clone https://github.com/w-bonelli/herbarium-sheets.git`, then build the image from the root directory with `docker build -t -f Dockerfile .`.
Alternatively, you can just pull the pre-built image with `docker pull wbonelli/herbarium-sheets`, or allow it to be pulled automatically from another Docker CLI command (as below).
## Usage
To analyze an image:
```bash
docker run wbonelli/herbarium-sheets python3.8 /opt/code/cli.py
```
By default, output files will be written to the current working directory. To specify a different output location, use `-o `.
## Development
To set up a development environment and explore or modify the source, just mount the project root as your container's working directory, for instance:
```bash
docker run -it -v $(pwd):/opt/dev -w /opt/dev wbonelli/herbarium-sheets bash
```
Then invoke the CLI with `python3.8 /opt/code/cli.py `.
Git is also instructed to ignore `data` and `output` directories for convenience.