ImageDataExtractor Documentation

ImageDataExtractor is a toolkit for the automatic extraction of data from microscopy images.

This guide provides a quick tour through ImageDataExtractor concepts and functionality.

Features

• Automatic detection and download of microscopy images from scientific articles
• HTML and XML document format support from RSC and Elsevier
• High-throughput capabilities
• Direct extraction from image files
• PNG, GIF, JPEG, TIFF image format support
• Automatic scalebar detection (reading and measurement)
• Particle segmentation with uncertainty quantification
• Particle sizes and radial distribution functions of extracted particle systems

Citing

If you use ImageDataExtractor as a resource in your research, please cite the following works:

K. T. Mukaddem, E. J. Beard, B. Yildirim, J. M. Cole, "ImageDataExtractor: A Tool to Extract and Quantify Data from Microscopy Images", J. Chem. Inf. Model. (2019) https://doi.org/10.1021/acs.jcim.9b00734

B. Yildirim, J. M. Cole, "Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification", J. Chem. Inf. Model. (2021) https://doi.org/10.1021/acs.jcim.0c01455

Funding

This project was financially supported by the Science and Technology Facilities Council (STFC) and the Royal Academy of Engineering (RCSRF1819\7\10).

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