[AVI 2020] Short Paper: BreastScreening

In this repository, we present the files from our published short paper [DOI: 10.1145/3399715.3399744] on the AVI 2020 (website) conference. The publication is related to our User Tests and Analysis 4 (UTA4) study. This repository also concerns the publication of several datasets regarding usability (SUS), workload (NASA-TLX), time, severity rates (BIRADS) and medical imaging results of clinicians from our User Tests and Analysis 4 (UTA4) study. That said, we created UTA4: SUS Dataset, UTA4: NASA-TLX Dataset, UTA4: Time Dataset, UTA4: Rates Dataset and UTA4: Medical Imaging DICOM Files Dataset pages to provide further information regarding these datasets and respective repositories. The paper is also available here (Read Only). A preprint version of this paper is available on ResearchGate [DOI: 10.13140/RG.2.2.28548.27523] and arXiv. The user tests were made in clinical institutions, where clinicians diagnose several patients for a Single-Modality vs Multi-Modality comparison. For example, in these tests, we used both prototype-single-modality and prototype-multi-modality repositories for the comparison. On the same hand, the hereby scientific publication represents the pieces of information of both BreastScreening and MIDA projects. These projects are research projects that deal with the use of a recently proposed technique in literature: Deep Convolutional Neural Networks (CNNs). From a developed User Interface (UI) and framework, these deep networks will incorporate several datasets in different modes. For more information about the available scientific publications please follow the Publications page on the Wiki of the meta information repository. Last but not least, you can find further information on the Wiki in this repository. We also have several demos to see in our YouTube Channel, please follow us.

Citing

We kindly ask scientific works and studies that make use of the repository to cite it in their associated publications. Similarly, we ask open-source and closed-source works that make use of the repository to warn us about this use.

You can cite our work using the following BibTeX entry:

@inproceedings{10.1145/3399715.3399744,
author = {Calisto, Francisco Maria and Nunes, Nuno and Nascimento, Jacinto C.},
title = {BreastScreening: On the Use of Multi-Modality in Medical Imaging Diagnosis},
year = {2020},
isbn = {9781450375351},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3399715.3399744},
doi = {10.1145/3399715.3399744},
abstract = {This paper describes the field research, design and comparative deployment of a multimodal medical imaging user interface for breast screening. The main contributions described here are threefold: 1) The design of an advanced visual interface for multimodal diagnosis of breast cancer (BreastScreening); 2) Insights from the field comparison of Single-Modality vs Multi-Modality screening of breast cancer diagnosis with 31 clinicians and 566 images; and 3) The visualization of the two main types of breast lesions in the following image modalities: (i) MammoGraphy (MG) in both Craniocaudal (CC) and Mediolateral oblique (MLO) views; (ii) UltraSound (US); and (iii) Magnetic Resonance Imaging (MRI). We summarize our work with recommendations from the radiologists for guiding the future design of medical imaging interfaces.},
booktitle = {Proceedings of the International Conference on Advanced Visual Interfaces},
articleno = {49},
numpages = {5},
keywords = {user-centered design, multimodality, medical imaging, human-computer interaction, healthcare systems, breast cancer, annotations},
location = {Salerno, Italy},
series = {AVI '20}
}

Prerequisites
Usage
Roadmap
Contributing
License & Copyright
Team
Acknowledgements

Abstract

This paper describes the field research, design and comparative deployment of a multimodal medical imaging user interface for breast screening. The main contributions described here are threefold: 1) The design of an advanced visual interface for multimodal diagnosis of breast cancer (BreastScreening); 2) Insights from the field comparison of single vs multimodality screening of breast cancer diagnosis with 31 clinicians and 566 images, and 3) The visualization of the two main types of breast lesions in the following image modalities: (i) MammoGraphy (MG) in both Craniocaudal (CC) and Mediolateral oblique (MLO) views; (ii) UltraSound (US); and (iii) Magnetic Resonance Imaging (MRI). We summarize our work with recommendations from the radiologists for guiding the future design of medical imaging interfaces.

Prerequisites

The following list is showing the required dependencies for this project to run locally:

Git or any other Git or GitHub version control tool
LaTeX

Here are some tutorials and documentation, if needed, to feel more comfortable about using and playing around with this repository:

Usage

Usage follow the instructions here to setup the current repository and extract the present data. To understand how the hereby repository is used for, read the following steps.

Installation

At this point, the only way to install this repository is manual. Eventually, this will be accessible through pip or any other package manager, as mentioned on the roadmap.

Nonetheless, this kind of installation is as simple as cloning this repository. Virtually all Git and GitHub version control tools are capable of doing that. Through the console, we can use the command below, but other ways are also fine.

git clone https://github.com/MIMBCD-UI/avi-2020-short-paper.git

Optionally, the module/directory can be installed into the designated Python interpreter by moving it into the site-packages directory at the respective Python directory.

Demonstration

Please, feel free to try out our source. It is a script called main.tex at the src/ directory. It can be used as follows:

latex src/main.tex

Roadmap

We need to follow the repository goal, by addressing the thereby information. Therefore, it is of chief importance to scale this solution supported by the repository. The repository solution follows the best practices, achieving the Core Infrastructure Initiative (CII) specifications.

Besides that, one of our goals involves creating a configuration file to automatically test and publish our code to pip or any other package manager. It will be most likely prepared for the GitHub Actions. Other goals may be written here in the future.

Contributing

This project exists thanks to all the people who contribute. We welcome everyone who wants to help us improve this downloader. As follows, we present some suggestions.

Issuer

Either as something that seems missing or any need for support, just open a new issue. Regardless of being a simple request or a fully-structured feature, we will do our best to understand them and, eventually, solve them.

Developer

We like to develop, but we also like collaboration. You could ask us to add some features… Or you could want to do it yourself and fork this repository. Maybe even do some side-project of your own. If the latter ones, please let us share some insights about what we currently have.

Information

The current information will summarize important items of this repository. In this section, we address all fundamental items that were crucial to the current information.

The following list, represents the set of related repositories for the presented one:

Dataset Resources

Associated with this scientific publication there are various public available datasets. To publish our datasets we used a well known platform called Kaggle. To access our project’s Profile Page just follow the link. For the purpose, three main resources uta4-singlemodality-vs-multimodality-nasatlx, uta4-sm-vs-mm-sheets and uta4-sm-vs-mm-sheets-nameless are published in this platform. Moreover, the Single-Modality vs Multi-Modality is available in our MIMBCD-UI Project page on data.world. Last but not least, datasets are also published at figshare and OpenML platforms.

License & Copyright

The avi-2020-short-paper repository is distributed under the terms of MIT license and CC-BY-SA-4.0 copyright. Permissions of this license are conditioned on making available complete elements from this repository of licensed works and modifications, which include larger works using a licensed work, under the same license. Copyright and license notices must be preserved.

Team

Our team brings everything together sharing ideas and the same purpose, developing even better work. In this section, we will nominate the full list of important people for this repository, as well as respective links.

Authors

Francisco Maria Calisto [ Website ResearchGate GitHub Twitter LinkedIn ]
Nuno Nunes [ Research Gate ]
Jacinto C. Nascimento [ Research Gate ]

Promoters

Hugo Lencastre
Nádia Mourão
Bruno Dias
Bruno Oliveira
Luís Ribeiro Gomes
Carlos Santiago

Acknowledgements

This work was partially supported by national funds through FCT and IST through the UID/EEA/50009/2013 project, BL89/2017-IST-ID grant. We thank Dr. Clara Aleluia and her radiology team of HFF for valuable insights and helping using the Assistant on their daily basis. From IPO-Lisboa, we would like to thank the medical imaging teams of Dr. José Carlos Marques and Dr. José Venâncio. From IPO-Coimbra, we would like to thank the radiology department director and the all team of Dr. Idílio Gomes. Also, we would like to provide our acknowledgments to Dr. Emília Vieira and Dr. Cátia Pedro from Hospital Santa Maria. Furthermore, we want to thank all team from the radiology department of HB for participation. Last but not least, a great thanks to Dr. Cristina Ribeiro da Fonseca, who among others is giving us crucial information for the BreastScreening project.

Supporting

Our organization is a non-profit organization. However, we have many needs across our activity. From infrastructure to service needs, we need some time and contribution, as well as help, to support our team and projects.