Loading
Official Round: Completed

ImageCLEF 2022 Tuberculosis - Caverns Report

1536
38
0
29

Note: ImageCLEF 2022 Tuberculosis includes 2 subtasks. This page is about the Caverns Report subtask. For information about the Caverns Detection subtask click here. Both challenges' datasets are shared together, so registering for one of these challenges will automatically give you access to the other one.

Note: Do not forget to read the Rules section on this page. Pressing the red Participate button leads you to a page where you have to agree with those rules. You will not be able to submit any results before agreeing with the rules.

Note: Before trying to submit results, read the Submission instructions section on this page.

Challenge description

Welcome to the 6th edition of the Tuberculosis Task!

Tuberculosis (TB) is a bacterial infection caused by a germ called Mycobacterium tuberculosis. About 130 years after its discovery, the disease remains a persistent threat and a leading cause of death worldwide according to WHO. This bacteria usually attacks the lungs, but it can also damage other parts of the body. Generally, TB can be cured with antibiotics. However, the different types of TB require different treatments, and therefore the detection of the TB type and characteristics are important real-world tasks.

Task history and lessons learned:

  • Tuberculosis task exists in ImageCLEF since 2017 and it was modified from year to year.
  • In the first and second editions of this task, held at ImageCLEF 2017 and ImageCLEF 2018, participants had to detect Multi-drug resistant patients (MDR subtask) and to classify the TB type (TBT subtask) both based only on the CT image. After 2 editions we concluded that the MDR subtask was not possible to solve based only on the image. In the TBT subtask, there was a slight improvement in 2018 with respect to 2017 on the classification results, however, not enough considering the amount of extra data provided in the 2018 edition, both in terms of new images and meta-data.
  • In the 3d edition Tuberculosis task was restructured to allow usage of uniform dataset, and included two subtasks - continued Severity Score (SVR) prediction subtask and a new subtask based on providing an automatic report (CT Report) on the TB case. In the 4th edition, the SVR subtask was dropped and automated CT report generation task was modified to be lung-based rather than CT-based. Because of fairly high results achieved by the participants in the CTR task in 4th edition, the task organizers have decided to discontinue the CTR task and brought back to life the Tuberculosis Type classification task from the 1st and 2nd ImageCLEFmed Tuberculosis editions to check if recent Machine Learning and Deep Learning methods allows to improve previous rather low results.

This challenge (subtask) is about the classification of caverns: participants must classify lung cavern regions in lung CT images associated with lung tuberculosis. The problem is important because even after successful treatment which fulfills the existing criteria of recovery the caverns may still contain colonies of Mycobacterium Tuberculosis that could lead to unpredictable disease relapse. Participants must predict 3 binary features of caverns suggested by experienced radiologists.

Data

The task dataset contains 60 train and 16 test cases. We understand that the data count for the subtask is small, so in case participants want to try deep learning approaches, we encourage them to use data from the Caverns Detection task for transfer learning. Any other public dataset usage is also welcome.

Each case includes the CT image, two versions of automatically extracted lung masks, information on cavern area location, and cavern report.

CT image

For all patients, we provide a single 3D CT image with an image size per slice of 512×512 pixels and the number of slices being around 100. 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 the 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, NiBabel package for Python.

Lungs mask

For all the CT images we provide two versions of automatically extracted masks of the lungs. These data can be downloaded together with the patients' CT images. The description of the first version of segmentation can be found here. The description of the second version of segmentation can be found here. The first version of segmentation provides more accurate masks, but it tends to miss large abnormal regions of lungs in the most severe TB cases. The second segmentation on the contrary provides more rough bounds, but behaves more stable in terms of including lesion areas. In case the participants use the provided masks in their experiments, please refer to the section "Citations" at the end of this page to find the appropriate citation for the corresponding lung segmentation technique.

Cavern area location

Cavern area location information includes a cavern area bounding box and cavern area centroid. This information is automatically extracted from manual segmentation masks. Please note, that source manual segmentation may have been done by different radiologists, therefore bounding boxes may be of different accuracy (for example, some margins may appear).  A single CT can have one or several cavern regions.

 

The file contains the following columns (header included):

id - train case id

bbox_X1, bbox_Y1, bbox_Z1 - coordinates of the first bounding box corner

bbox_X2, bbox_Y2, bbox_Z2 - coordinates of the second (diagonal) bounding box corner

centroid_X, centroid_Y, centroid_Z - coordinates of the cavern area centroid

 

Cavern report

 

Cavern report includes 3 manually labeled binary features, which describe the case' cavern(s).

The features are 1) presence of thick walls, 2) presence of calcifications, 3) presence of foci around the cavern.

These features are the prediction target in the task.

 

The report is provided as a simple .csv file, containing the following columns (header included):

ID - train case id

thick_walls - binary label for the presence of thick walls around the cavern

has_calcification - binary label for the presence of calcifications around the cavern 

foci_around - binary label for the presence of foci around the cavern


As soon as the data are released they will be available under the "Resources" tab.


Submission instructions


As soon as the submission is open, you will find a “Create Submission” button on this page (next to the tabs).


Before being allowed to submit your results, you have to first press the red participate button, which leads you to a page where you have to accept the challenge's rules.


Submit a plain text file with the following format:

<Filename>,<Probablity of the thick walls presence>,<Probablity of the calcification presence>,<Probablity of the foci presence>

e.g.:

TST_01.nii.gz,0.89,0.1,0.84

TST_02.nii.gz,0.88,0.78,0.59

.....

You need to respect the following constraints:

File should not have a header.

Filenames must be same as original test file names

All filenames must be present in the runfiles

Only use numbers between 0 and 1 for the probabilities. Use the dot (.) as a decimal point (no commas accepted)

Evaluation criteria

This task is considered a multi-binary classification problem.

The ranking of this task will be done first by mean AUC and then by min AUC over the 3 target labels.

Rules


Note: In order to participate in this challenge you have to sign an End User Agreement (EUA). You will find more information on the 'Resources' tab.


ImageCLEF lab is part of the Conference and Labs of the Evaluation Forum: CLEF 2022. CLEF 2022 consists of independent peer-reviewed workshops on a broad range of challenges in the fields of multilingual and multimodal information access evaluation, and a set of benchmarking activities carried in various labs designed to test different aspects of mono and cross-language Information retrieval systems. More details about the conference can be found here.

Submitting a working note with the full description of the methods used in each run is mandatory. Any run that could not be reproduced thanks to its description in the working notes might be removed from the official publication of the results. Working notes are published within CEUR-WS proceedings, resulting in an assignment of an individual DOI (URN) and an indexing by many bibliography systems including DBLP. According to the CEUR-WS policies, a light review of the working notes will be conducted by ImageCLEF organizing committee to ensure quality. As an illustration, ImageCLEF 2021 working notes (task overviews and participant working notes) can be found within CLEF 2021 CEUR-WS proceedings.

Important

Participants of this challenge will automatically be registered at CLEF 2022. In order to be compliant with the CLEF registration requirements, please edit your profile by providing the following additional information:

  • First name

  • Last name

  • Affiliation

  • Address

  • City

  • Country

  • Regarding the username, please choose a name that represents your team.

This information will not be publicly visible and will be exclusively used to contact you and to send the registration data to CLEF, which is the main organizer of all CLEF labs

Participating as an individual (non affiliated) researcher

We welcome individual researchers, i.e. not affiliated to any institution, to participate. We kindly ask you to provide us with a motivation letter containing the following information:

  • the presentation of your most relevant research activities related to the task/tasks

  • your motivation for participating in the task/tasks and how you want to exploit the results

  • a list of the most relevant 5 publications (if applicable)

  • the link to your personal webpage

The motivation letter should be directly concatenated to the End User Agreement document or sent as a PDF file to bionescu at imag dot pub dot ro. The request will be analyzed by the ImageCLEF organizing committee. We reserve the right to refuse any applicants whose experience in the field is too narrow, and would therefore most likely prevent them from being able to finish the task/tasks.

Citations

Information will be posted after the challenge ends.

Prizes

Publication

ImageCLEF 2022 is an evaluation campaign that is being organized as part of the CLEF initiative labs. The campaign offers several research tasks that welcome participation from teams around the world. The results of the campaign appear in the working notes proceedings, published by CEUR Workshop Proceedings (CEUR-WS.org). Selected contributions among the participants will be invited for publication in the following year in the Springer Lecture Notes in Computer Science (LNCS) together with the annual lab overviews.

Resources

Contact us

Discussion Forum

Alternative channels

We strongly encourage you to use the public channels mentioned above for communications between the participants and the organizers. In extreme cases, if there are any queries or comments that you would like to make using a private communication channel, then you can send us an email at :

  • kozlovski [dot] serge [at] gmail [dot] com
  • vitali [dot] liauchuk [at] gmail [dot] com
  • yashin [dot] dicente [at] warwick [dot] ac [dot] uk

More information

You can find additional information on the challenge here: https://www.imageclef.org/2022/medical/tuberculosis

Participants