A toolkit for extracting particle data from microscopy images.
ImageDataExtractor is a toolkit for the automatic extraction of microscopy images.
- Automatic detection and download of microscopy images from scientific articles
- HTML and XML document format support
- High-throughput capabilities
- Direct extraction from image files
- PNG, GIF, JPEG, TIFF image format support
It is best to install ImageDataExtractor using pip, but it is also possible to directly install from source. See below for installation instructions.
__NOTE: The current version of IDE uses Tesseract 3. The source code can be downloaded [here](https://github.com/tesseract-ocr/tesseract/tree/3.05) and instructions on how to compile can be found [here](https://github.com/tesseract-ocr/tesseract/wiki/Compiling).__
NOTE: It is advised that all installations of ImageDataExtractor are run inside a virtual environment. Click [here](https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/) for more information.
### Installing with pip
To install with pip, simply run:
pip install ImageDataExtractor
Then download the necessary data files to run ChemDataExtractor-IDE by running:
cde data download
### Installing from source
#### Install ChemDataExtractor-IDE
In order to use ImageDataExtractor first install the bespoke version of ChemDataExtractor, [ChemDataExtractor-IDE](https://github.com/edbeard/chemdataextractor-ide).
Clone the repository by running:
and install with:
$ python setup.py install
Then download the required machine learning models with:
$ cde data download
See https://github.com/edbeard/chemdataextractor-ide for more details
#### Install ImageDataExtractor
Now to install ImageDataExtractor, clone the repository with:
$ git clone https://github.com/ktm2/ImageDataExtractor.git
Then create a wheel file by running:
$ python setup.py bdist_wheel
You may have to run `pip install wheel` if this fails.
Then install using pip:
$ pip install dist/ImageDataExtractor-0.0.1-py3-none-any.whl
## Running the code
__Full documentation on running the code can be found at [www.imagedataextractor.org](https://www.imagedataextractor.org) .__
Open a python terminal and run
>>> import imagedataextractor as ide
to automatically identify and extract the images from a document. Full details on supported input and output formats can be found at our [website](https://www.imagedataextractor.org) .
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