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ImageCLEFtuberculosis

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Motivation

About 130 years after the discovery of Mycobacterium tuberculosis, the disease remains a persistent threat and a leading cause of death worldwide. The greatest disaster that can happen to a patient with tuberculosis (TB) is that the organisms become resistant to two or more of the standard drugs. In contrast to drug sensitive (DS) tuberculosis, its multi-drug resistant (MDR) form is much more difficult and expensive to recover from. Thus, early detection of the drug resistance (DR) status is of great importance for effective treatment. The most commonly used methods of DR detection are either expensive or take too much time (up to several month). Therefore there is a need for quick and at the same time cheap methods of DR detection. One of the possible approaches for this task is based on Computed Tomography (CT) image analysis.
Another challenging task is automatic detection of TB types using CT volumes.
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News

  • 1.2.2017:training data for the two tasks are made available
  • 17.11.2016:first information on the task being available on the web pages

Participant registration

Registration for ImageCLEF 2017 is now open and will stay open until at least 21.04.2017. To register please follow the steps below:

Once registered and the signature validated, data access details can be found in the ImageCLEF system -> Collections. Please note that depending on the task, before downloading the data, you may be required for signing some additional data usage agreements. Should you have any questions about the registration process, please contact Mihai Dogariu <dogariu_mihai8(at)yahoo.com>.

Schedule

  • 15.11.2016: registration opens for all ImageCLEF tasks (until 22.04.2016)
  • 01.02.2017: development data release starts
  • 15.03.2017: test data release starts
  • 04.05.2017: deadline for submission of runs by the participants
  • 15.05.2017: release of processed results by the task organizers
  • 26.05.2017: deadline for submission of working notes papers by the participants
  • 17.06.2017: notification of acceptance of the working notes papers
  • 01.07.2017: camera ready working notes papers
  • 11.-14.09.2017: CLEF 2017, Dublin, Ireland

Subtasks Overview

The ImageCLEFtuberculosis task includes two independent subtasks.

Subtask #1: MDR Detection

The goal of this subtask is to assess the probability of a TB patient having resistant form of tuberculosis based on the analysis of chest CT scan.

Subtask #2: Detection of TB Type

The goal of this subtask is to automatically categorize each TB case into one of the following five types: Infiltrative, Focal, Tuberculoma, Miliary, Fibro-cavernous.

Data collection

Subtask #1: MDR Detection

For subtask #1, a dataset of 3D CT images is used along with a set of clinically relevant metadata. The dataset includes only HIV-negative patients with no relapses and having one of the two forms of tuberculosis: drug sensitive (DS) or multi-drug resistant (MDR).

# Patients Train Test
DS 134 101
MDR 96 113
Total patients 230 214

Subtask #2: Detection of TB Type

The dataset used in subtask #2 includes chest CT scans of TB patients along with the TB type.

# Patients Train Test
Type 1 140 80
Type 2 120 70
Type 3 100 60
Type 4 80 50
Type 5 60 40
Total patients 500 300

For both subtasks we provide 3D CT images with slice size of 512*512 pixels and number of slices varying from about 50 to 400. All the CT images are stored in NIFTI file format with .nii.gz file extension (g-zipped .nii files). This file format stores raw voxel intensities in Hounsfield units (HU) as well the corresponding image metadata such as image dimensions, voxel size in physical units, slice thickness, etc. A freely-available tool called "VV" can be used for viewing image files. Currently, there are various tools available for reading and writing NIFTI files. Among them there are load_nii and save_nii functions for Matlab and Niftilib library for C, Java, Matlab and Python.

Moreover, for all patients in both subtasks we provide automatic extracted masks of the lungs. This material can be downloaded together with the patients CT images. The details of this segmentation can be found here.
In case the participants use these masks in their experiments, please refer to the section "Citations" at the end of this page to find the appropriate citation for this lung segmentation technique.

Submission instructions

Disclaimer: This section is not final yet and may be subject to changes
Please note that each group is allowed a maximum of 10 runs per subtask.

Subtask #1: MDR Detection

Submit a plain text file named with the prefix MDR (e.g. MDRfree-text.txt) with the following format:

  • <Patient-ID>,<Probability of MDR>

e.g.:

  • MDR_TST_001,0.1
  • MDR_TST_002,1
  • MDR_TST_003,0.56
  • MDR_TST_004,0.02

Please use a score between 0 and 1 to indicate the probability of the patient having MDR

You need to respect the following constraints:

  • Only use numbers between 0 and 1 for the score. Use the dot (.) as a decimal point (no commas accepted)
  • Patient-IDs must be part of the predefined Patient-IDs
  • All patient-IDs must be present in the runfiles


Subtask #2: Detection of TB Type

Submit a plain text file named with the prefix TBT (e.g. TBTfree-text.txt) with the following format:

  • <Patient-ID>,<TB-Type>

e.g.:

  • TBT_TST_501,1
  • TBT_TST_502,3
  • TBT_TST_503,5
  • TBT_TST_504,4
  • TBT_TST_505,2

Please use the following Codes for the TB types:

  • 1 for Infiltrative
  • 2 for Focal
  • 3 for Tuberculoma
  • 4 for Miliary
  • 5 for Fibro-cavernous
  • You need to respect the following constraints:

    • Only use the defined codes for the various TB types
    • Only use one TB type per patient
    • PatientIDs must be part of the predefined Case-IDs
    • All patient-IDs must be present in the runfiles

    Evaluation methodology

    Subtask #1: MDR Detection

    The results will be evaluated using ROC-curves produced from the probabilities provided by participants.

    Subtask #2: Detection of TB Type

    The results will be evaluated using unweighted Cohen’s Kappa (sample Matlab code).

    Citations

    • When referring to the ImageCLEFmed 2017 task general goals, general results, etc. please cite the following publication which will be published by September 2017:
    • When referring to ImageCLEFmed task in general, please cite the following publication:
      • Jayashree Kalpathy-Cramer, Alba García Seco de Herrera, Dina Demner-Fushman, Sameer Antani, Steven Bedrick and Henning Müller, Evaluating Performance of Biomedical Image Retrieval Systems –an Overview of the Medical Image Retrieval task at ImageCLEF 2004-2014 (2014), in: Computerized Medical Imaging and Graphics
      • BibText:

        @Article{KGD2014,
          Title = {Evaluating Performance of Biomedical Image Retrieval Systems-- an Overview of the Medical Image Retrieval task at {ImageCLEF} 2004--2014},
          Author = {Kalpathy--Cramer, Jayashree and Garc\'ia Seco de Herrera, Alba and Demner--Fushman, Dina and Antani, Sameer and Bedrick, Steven and M\"uller, Henning},
          Journal = {Computerized Medical Imaging and Graphics},
          Year = {2014}

        }

    • When using the provided mask of the lungs , please cite the following publication:
      • Yashin Dicente Cid, Oscar A. Jiménez-del-Toro, Adrien Depeursinge, and Henning Müller, Efficient and fully automatic segmentation of the lungs in CT volumes. In: Goksel, O., et al. (eds.) Proceedings of the VISCERAL Challenge at ISBI. No. 1390 in CEUR Workshop Proceedings (Apr 2015)
      • BibText:

        @inproceedings{DJD2015,
          title = {Efficient and fully automatic segmentation of the lungs in {CT} volumes},
          booktitle = {Proceedings of the {VISCERAL} Anatomy Grand Challenge at the 2015 {IEEE ISBI}},
          author = {Dicente Cid, Yashin and Jim{\'{e}}nez del Toro, Oscar Alfonso and Depeursinge, Adrien and M{\"{u}}ller, Henning},
          editor = {Goksel, Orcun and Jim{\'{e}}nez del Toro, Oscar Alfonso and Foncubierta-Rodr{\'{\i}}guez, Antonio and M{\"{u}}ller, Henning},
          keywords = {CAD, lung segmentation, visceral-project},
          month = may,
          series = {CEUR Workshop Proceedings},
          year = {2015},
          pages = {31-35},
          publisher = {CEUR-WS},
          location = {New York, USA},
          url = {http://ceur-ws.org/Vol-1390/}
          }

        }

    Organizers

    Acknowledgements