CSIM Toolkit - ITK

This is a repository for ITK modules develped by the Computing in Signals and Images in Medicine Laboratory (CSIM). Here it is available the C++ source code for each application, where you can download and adapt for your needs. Additionally, if you want purpose an improvement for any of our methods, please fork this repository and send us a pull request.

For more details about ITK, see to website.

Available Methods

Each method implemented here are organized in different categories, following the ITK style.

Module: Filtering

• Anisotropic Anomalous Diffusion (AAD)
• Isotropic Anomalous Diffusion (IAD)

Module: Features

• Diffusion Complexity Mapping
• Diffusion Entropy Mapping
• Sample Entropy 2D
• Logistic Contrast Enhancement
• Image Quality Metrics
• Automatic Conductance Image Calculator
• Global Logistic Contrast Enhancement Image Filter

Module: Segmentation

• Generalized Entropy Threshold
• Multiple Logistic Classification

Installation Procedure

A simple code provided in the Example folder could be used as guide for the usage of all the tools provided in this repository. The easiest way is to compile the code using CMake and following the instructions in the Main.cpp file.

Documentation

Some of our methods have been published in the Insight Journal and it could be useful for documentation. However, not all the methods in this repository have a documentation file and, in case of any help, enter in contact with one of our laboratory members (see Contact section).

Citation and References

All methods are under the ITK license. However, if you use any of this methods in your own research, please cite it properly. Details about the correct reference to cite each method are provided in the following list:

Anomalous Diffusion Filters

Anomalous Diffusion Paradigm for Image Denoising Process, Insight-Journal, 2016

Anomalous diffusion process applied to magnetic resonance image enhancement, Physics in Medicine and Biology, 2015

Sample Entropy 2D

Two-dimensional sample entropy: assessing image texture through irregularity, Biomedical Physics & Engineering Express, 2016

Automatic Conductance Image Calculator

Automatic Conductance Estimation Methods for Anisotropic Diffusion ITK Filters, Insight-Journal, 2017

Logistic Contrast Enhancement

A hybrid approach based on logistic classification and iterative contrast enhancement algorithm for hyperintense Multiple Sclerosis lesion segmentation, Medical & Biological Engineering & Computing, 2017

Multiple Logistic Classification

Extracting Image Objects by Multiple Logistic Classification Algorithm, Insight-Journal, 2017

Global Logistic Contrast Enhancement Image Filter

..., Insight-Journal, 2018

Contact

This repository is provided by the CSIM research group and if you want to give us a feedback or report a problem, please send an email to:

Ph.D. Antonio Carlos da S. Senra Filho: email, ResearchGate

Prof. Ph.D. Luiz Otavio Murta Junior (PI): email, ResearchGate

or enter in our group website to see more details about our research projects!