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Image processing for seed images

Project description

# Sid
## Image processing for seed images

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Python script for image processing of plant seed images, specifically _Lamium amplexicaule_.

[![Supported Python versions](](
[![Build Status](](

## Requirements

- Python 2.7
- PIL/Pillow
- numpy
- scipy.ndimage
- scikit-image
- matplotlib
- watchdog
- click

For testing and documentation:

- nose
- coverage
- sphinx

## Install

1. Install the [Anaconda Python 2.7 distribution](
1. Install Sid using pip:
pip install Sid
1. Check that Sid was installed properly:
take_cover --version

### Developers

Sid can also be used by cloning the repository, usually for developing purposes:
git clone
or by downloading the repository as a [zip file](

## Usage

### take_cover

Use by running:
The script will first ask for a folder name - this will be the working directory from which the script will read _jpg_ files and to which it will write _png_ and _csv_ files.

The script will then ask if the folder should be prcoessed Continuously or once.

For more options, see the help message:
take_cover --help

## Continuous processing

In this case the script will wait for new _jpg_ files in the folder. When a new _jpg_ file is created, the script will process it, creating _png_ files with the color spaces and the segmentation checkpoints, open the segmentation image, and will print the final stats to the screen.

## Single processing

In this case the script will go over all _jpg_ files in the folder and process them. It will produce _png_ files with the color spaces and the segmentation checkpoints and two _csv_ files: one with the final stats for each _jpg_ file and one with the histograms that were used to find the features on the seed (background, eliosom, cover).

### take_cover.json

This is the configuration file which includes values of different parameters of the algorithm, including segmentation thresholds.

## Support
Don't hesitate to contact [Yoav Ram]( for questions and help.

Bugs and feature requests can be opened on [GitHub](

[![GitHub issues](](

## License

Sid source code and examples are licensed under the terms of the [MIT license](

Sid documentation, examples, and other materials are licensed under the terms of the [Creative Commons Attribution 4.0 International (CC BY 4.0) license](

Project details

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