MPE_tool

Mammogram Patches Extraction tool

This tool can be used for the extraction of patches from three open and well known datasets (INbreast, mini-MIAS and CBIS_DDSM) containing digital or digitized mammograms.

Required Libraries:

 random, cv2, matplotlib, PIL, numpy, pydicom, anot_core

Note: The anot_core library can be installed using the following command:

pip3 install git+https://github.com/itzortzis/MPE_tool.git

Files and description:

MPE_tool
│    README.md
│
└─── MPE_core
│    │   mpe.py  #The main file containing the ImgPatchExtractor class
│   
│   
└─── notebook
     │   mpe.ipynb #Colab/Jupyter notebook version of the tool

Installation

---

The MPE_tool can be cloned from here or it can be installed using Python pip tool

• Option 1: Clone the repository and see the demo files in python and notebook folders
• Option 2:
  • Install tool using pip3 install git+https://github.com/itzortzis/MPE_tool.git
  • Import the needed components from MPE_core import mpe

Enjoy!!!

INBreast dataset:

Inês C. Moreira, Igor Amaral, Inês Domingues, António Cardoso, Maria João Cardoso, Jaime S. Cardoso, INbreast: Toward a Full-field Digital Mammographic Database, Academic Radiology, Volume 19, Issue 2, 2012, Pages 236-248, ISSN 1076-6332, https://doi.org/10.1016/j.acra.2011.09.014. (https://www.sciencedirect.com/science/article/pii/S107663321100451X)

mini-MIAS dataset:

J Suckling et al (1994), MINI-MIAS: The Mammographic Image Analysis Society Digital Mammogram Database Exerpta Medica, International Congress, Series 1069, pp375-378. http://peipa.essex.ac.uk/info/mias.html

CBIS_DDSM:

Lee, R. S., Gimenez, F., Hoogi, A., Miyake, K. K., Gorovoy, M., & Rubin, D. L. (2017), CBIS_DDSM: A curated mammography data set for use in computer-aided detection and diagnosis research, In Scientific Data (Vol. 4, Issue 1), Springer Science and Business Media LLC, https://doi.org/10.1038/sdata.2017.177