Using Crowdsourcing for Multi-label Biomedical Compound Figure Annotation

Information analysis or retrieval for images in the biomedical literature needs to deal with a large amount of compound figures (figures containing several subfigures), as they constitute probably more than half of all images in repositories such as PubMed Central, which was the data set used for the task. The ImageCLEFmed benchmark proposed among other tasks in 2015 and 2016 a multi-label classification task, which aims at evaluating the automatic classification of figures into 30 image types. This task was based on compound figures and thus the figures were distributed to participants as compound figures but also in a separated form. Therefore, the generation of a gold standard was required, so that algorithms of participants can be evaluated and compared. This work presents the process carried out to generate the multi-labels of ∼2650 compound figures using a crowdsourcing approach. Automatic algorithms to separate compound figures into subfigures were used and the results were then validated or corrected via crowdsourcing. The image types (MR, CT, X–ray, ...) were also annotated by crowdsourcing including detailed quality control. Quality control is necessary to insure quality of the annotated data as much as possible. ∼625 h were invested with a cost of ∼870$

Large-scale medical image annotation with quality-controlled crowdsourcing

Accurate annotations of medical images are essential for various clinical applications. The remarkable advances in machine learning, especially deep learning based techniques, show great potential for automatic image segmentation. However, these solutions require a huge amount of accurately annotated reference data for training. Especially in the domain of medical image analysis, the availability of domain experts for reference data generation is becoming a major bottleneck for machine learning applications. In this context, crowdsourcing has gained increasing attention as a tool for low-cost and large-scale data annotation. As a method to outsource cognitive tasks to anonymous non-expert workers over the internet, it has evolved into a valuable tool for data annotation in various research fields. Major challenges in crowdsourcing remain the high variance in the annotation quality as well as the lack of domain specific knowledge of the individual workers. Current state-of-the-art methods for quality control usually induce further costs, as they rely on a redundant distribution of tasks or perform additional annotations on tasks with already known reference outcome. Aim of this thesis is to apply common crowdsourcing techniques for large-scale medical image annotation and create a cost effective quality control method for crowd-sourced image annotation. The problem of large-scale medical image annotation is addressed by introducing a hybrid crowd-algorithm approach that allowed expert-level organ segmentation in CT scans. A pilot study performed on the case of liver segmentation in abdominal CT scans showed that the proposed approach is able to create organ segmentations matching the quality of those create by medical experts. Recording the behavior of individual non-expert online workers during the annotation process in clickstreams enabled the derivation of an annotation quality measure that could successfully be used to merge crowd-sourced segmentations. A comprehensive validation study performed with various object classes from publicly available data sets demonstrated that the presented quality control measure generalizes well over different object classes and clearly outperforms state-of-the-art methods in terms of costs and segmentation quality. In conclusion, the methods introduced in this thesis are an essential contribution to reduce the annotation costs and further improve the quality of crowd-sourced image segmentation

A Survey of Crowdsourcing in Medical Image Analysis

Rapid advances in image processing capabilities have been seen across many domains, fostered by the application of machine learning algorithms to "big-data". However, within the realm of medical image analysis, advances have been curtailed, in part, due to the limited availability of large-scale, well-annotated datasets. One of the main reasons for this is the high cost often associated with producing large amounts of high-quality meta-data. Recently, there has been growing interest in the application of crowdsourcing for this purpose; a technique that a technique that is well established in a number of disciplines, including astronomy, ecology and meteorology for creating large-scale datasets across a range of disciplines, from computer vision to astrophysics. Despite the growing popularity of this approach, there has not yet been a comprehensive literature review to provide guidance to researchers considering using crowdsourcing methodologies in their own medical imaging analysis. In this survey, we review studies applying crowdsourcing to the analysis of medical images, published prior to July 2018. We identify common approaches and challenges and provide recommendations to researchers implementing crowdsourcing for medical imaging tasks. Finally, we discuss future opportunities for development within this emerging domain

BIAS: Transparent reporting of biomedical image analysis challenges

The number of biomedical image analysis challenges organized per year is steadily increasing. These international competitions have the purpose of benchmarking algorithms on common data sets, typically to identify the best method for a given problem. Recent research, however, revealed that common practice related to challenge reporting does not allow for adequate interpretation and reproducibility of results. To address the discrepancy between the impact of challenges and the quality (control), the Biomedical Image Analysis ChallengeS (BIAS) initiative developed a set of recommendations for the reporting of challenges. The BIAS statement aims to improve the transparency of the reporting of a biomedical image analysis challenge regardless of field of application, image modality or task category assessed. This article describes how the BIAS statement was developed and presents a checklist which authors of biomedical image analysis challenges are encouraged to include in their submission when giving a paper on a challenge into review. The purpose of the checklist is to standardize and facilitate the review process and raise interpretability and reproducibility of challenge results by making relevant information explicit