imagedataextractor is a Python library for electron microscopy image quantification.
imagedataextractor is a Python library for nanoparticle electron microscopy image quantification.
Try the online Demo.
- Automatic detection and download of microscopy images from scientific articles.
- Particle segmentation with uncertainty quantification.
- Particle localization.
- Automatic scalebar detection (reading and measurement).
- Particle size distributions.
- Locations, sizes and aspect ratios of all particles in an image (in the form of a .csv file).
- Radial distribution functions of extracted particle systems.
imagedataextractor requires Python 3.7 or above. We strongly recommend the use of a virtual environment for installation, as imagedataextractor requires specific versions of its requirements to be installed in order to function as intended.
sudo apt-get install tesseract-ocr libtesseract-dev
pip install imagedataextractor
Installation from source
- Clone the repo and move into the directory:
git clone https://github.com/by256/imagedataextractor.git cd imagedataextractor
Activate your virtual environment.
python setup.py install
Simply provide as input a path to an image or a document, or a path to a directory of images and/or documents.
import imagedataextractor as ide image_path = '<path/to/image>' data = ide.extract(image_path) # view extracted data as a pandas DataFrame df = data.to_pandas() # retrieve extracted scalebar data sb_text = data.scalebar.text conversion = data.scalebar.conversion # pixels to meters # resulting particle segmentations seg = data.segmentation
If the input image is a figure containing a panel of images, these will be split and extraction will be performed on each sub-image separately.
If you use imagedataextractor in your work, please cite the following works:
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
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
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size||File type||Python version||Upload date||Hashes|
|Filename, size imagedataextractor-2.0.4-py3-none-any.whl (98.3 MB)||File type Wheel||Python version py3||Upload date||Hashes View|
|Filename, size imagedataextractor-2.0.4.tar.gz (18.2 kB)||File type Source||Python version None||Upload date||Hashes View|
Hashes for imagedataextractor-2.0.4-py3-none-any.whl