ImageDataExtractor 2.0 is available as an open source python package. Installation using pip is highly recommended.

Download the latest release below. For help with installation and getting started, check out the documentation.

December 2020
Latest release

ImageDataExtractor 2.0

Source code for the ImageDataExtractor 2.0 toolkit.


Electron Microscopy Particle Segmentation (EMPS) Dataset


Download the data used to train the particle segmentation module of ImageDataExtractor 2.0. EMPS is the first human-labeled particle instance segmentation dataset, consisting of 465 electron microscopy images and associated semantic-instance segmentation maps. The data can also be downloaded from the EMPS Github repo.

B. Yildirim, J. M. Cole, "Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification", J. Chem. Inf. Model. (2021)
December 2020

EMPS Dataset

A .zip file containing images, segmentation maps and metadata files.


ImageDataExtractor 1.01 Evaluation files

ImageDataExtractor 1.01 performance was evaluated as part of the following publication:

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)
27th August 2019

ImageDataExtractor evaluation corpus

A CSV file containing the Digital Object Indentifier (DOI) and figure number for each file in the corpus used to evaluate the performance of ImageDataExtractor.