MISS-tool: medical image segmentation synthesis tool

General Information

MISS-tool is a MATLAB-based package to emulate contours with certain segmentation errors based on a user-specified truth mask. The MISS-tool also provides the segmentation evaluation results of 24 segmentation performance metrics (see [ref] for a full list), including the Dice coefficient, Jaccard index (IoU), Medical Similarity Index (MSI), and several distance-based metrics. The tool can be used for:

• Segmentation performance evaluation: the user inputs a segmentation result and a reference standard (a.k.a truth) segmentation and the program outputs performance metrics chosen by the user.
• Image segmentation synthesis: the user inputs a truth mask and the program outputs a segmentation contour with segmentation errors controlled by tunable parameters. The synthetic contours can be used, for example, to investigate the response of performance metrics to certain segmentation errors, thus informing the user to choose appropriate metrics for their applications [ref].

The tool can be used in two ways:

• Graphical User Interface (GUI): the GUI allows for visualization of the synthesis results, interactively tuning synthesis parameters, and evaluation results. It includes:

  • Computing Segmentation Metrics
  • Synthesis of Segmentation Contours

• Command-line Functions: the command-line mode allows for processing images in batches as well as providing flexible ways for users to integrate the MISS tool with their applications. It includes:

  • Functions for segmentation evaluation metrics
  • Functions for segmentation synthesis

Installation

This section will help you to install the packages needed for MISS-tool.

Pre-requirements

Installed the MATLAB R2023b or later versions.

Preparation

• Download the whole repository from its GitHub and put all files as their original structure in a folder (named "MISS-tool").

https://github.com/didsr/MISS-tool

• Use GUI

  • Open the main_option.mlapp file with MATLAB.
  • Click the "Run" button to strat the GUI.
  

• Use Command-line Functions

  • Set the "Current Folder" in MATLAB as "MISS-tool"
  • Run commands in the "Command Window" in MATLAB
  • Alternatively, create "New Script" or "New Live Script" in MATLAB, and save them in the (root directory of) "MISS-tool" folder.

User's Manual

User's Manual: Link

Testing Examples

• Segmentation evaluation
• Segmentation synthesis

Cite this repository

If you find that MISS-tool is useful or if you use it in your project, please consider citing the code:

https://github.com/didsr/MISS-tool

And this paper:

@inproceedings{10.1117/12.2653650,
author = {Shuyue Guan and Ravi K. Samala and Arian Arab and Weijie Chen},
title = {{MISS-tool: medical image segmentation synthesis tool to emulate segmentation errors}},
volume = {12465},
booktitle = {Medical Imaging 2023: Computer-Aided Diagnosis},
editor = {Khan M. Iftekharuddin and Weijie Chen},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {1246518},
keywords = {Medical Image Segmentation Synthesis, Manual Segmentation Emulation, Segmentation Evaluation, Segmentation Errors},
year = {2023},
doi = {10.1117/12.2653650},
URL = {https://doi.org/10.1117/12.2653650}
}

Auxiliary Files

The sample data are from the LIDC-IDRI dataset, grouped by slices and including fused labels using STAPLE and MV, can be found here.

Contact

For any questions/suggestions/collaborations regarding this tool, please contact Shuyue Guan ([email protected]) or Weijie Chen ([email protected]).

Acknowledgment

• This project was supported in part by an appointment to the ORISE Research Participation Program at the Center for Devices and Radiological Health, U.S. Food and Drug Administration, administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and FDA/CDRH.