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- Breznik, Eva, et al.
(författare)
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Effects of distance transform choice in training with boundary loss
- 2021
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Convolutional neural networks are the method of choice for many medical imaging tasks, in particular segmentation. Recently, efforts have been made to include distance measures in the network training, as for example the introduction of boundary loss, calculated via a signed distance transform. Using boundary loss for segmentation can alleviate issues with imbalance and irregular shapes, leading to a better segmentation boundary. It is originally based on the Euclidean distance transform. In this paper we investigate the effects of employing various definitions of distance when using the boundary loss for medical image segmentation. Our results show a promising behaviour in training with non-Euclidean distances, and suggest a possible new use of the boundary loss in segmentation problems.
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- Breznik, Eva
(författare)
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Image Processing and Analysis Methods for Biomedical Applications
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- With new technologies and developments medical images can be acquired more quickly and at a larger scale than ever before. However, increased amount of data induces an overhead in the human labour needed for its inspection and analysis. To support clinicians in decision making and enable swifter examinations, computerized methods can be utilized to automate the more time-consuming tasks. For such use, methods need be highly accurate, fast, reliable and interpretable. In this thesis we develop and improve methods for image segmentation, retrieval and statistical analysis, with applications in imaging-based diagnostic pipelines. Individual objects often need to first be extracted/segmented from the image before they can be analysed further. We propose methodological improvements for deep learning-based segmentation methods using distance maps, with the focus on fully-supervised 3D patch-based training and training on 2D slices under point supervision. We show that using a directly interpretable distance prior helps to improve segmentation accuracy and training stability.For histological data in particular, we propose and extensively evaluate a contrastive learning and bag of words-based pipeline for cross-modal image retrieval. The method is able to recover correct matches from the database across modalities and small transformations with improved accuracy compared to the competitors. In addition, we examine a number of methods for multiplicity correction on statistical analyses of correlation using medical images. Evaluation strategies are discussed and anatomy-observing extensions to the methods are developed as a way of directly decreasing the multiplicity issue in an interpretable manner, providing improvements in error control. The methods presented in this thesis were developed with clinical applications in mind and provide a strong base for further developments and future use in medical practice.
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- Breznik, Eva, et al.
(författare)
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Multiple comparison correction methods for whole-body magnetic resonance imaging
- 2020
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Ingår i: Journal of Medical Imaging. - : SPIE-Intl Soc Optical Eng. - 2329-4302 .- 2329-4310. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Voxel-level hypothesis testing on images suffers from test multiplicity. Numerous correction methods exist, mainly applied and evaluated on neuroimaging and synthetic datasets. However, newly developed approaches like Imiomics, using different data and less common analysis types, also require multiplicity correction for more reliable inference. To handle the multiple comparisons in Imiomics, we aim to evaluate correction methods on whole-body MRI and correlation analyses, and to develop techniques specifically suited for the given analyses. Approach: We evaluate the most common familywise error rate (FWER) limiting procedures on whole-body correlation analyses via standard (synthetic no-activation) nominal error rate estimation as well as smaller prior-knowledge based stringency analysis. Their performance is compared to our anatomy-based method extensions. Results: Results show that nonparametric methods behave better for the given analyses. The proposed prior-knowledge based evaluation shows that the devised extensions including anatomical priors can achieve the same power while keeping the FWER closer to the desired rate. Conclusions: Permutation-based approaches perform adequately and can be used within Imiomics. They can be improved by including information on image structure. We expect such method extensions to become even more relevant with new applications and larger datasets.
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- Bäcklin, Emelie, et al.
(författare)
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Pulmonary volumes and signs of chronic airflow limitation in quantitative computed tomography
- 2024
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Ingår i: Clinical Physiology and Functional Imaging. - : Wiley. - 1475-0961 .- 1475-097X. ; 44:4, s. 340-348
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundComputed tomography (CT) offers pulmonary volumetric quantification but is not commonly used in healthy individuals due to radiation concerns. Chronic airflow limitation (CAL) is one of the diagnostic criteria for chronic obstructive pulmonary disease (COPD), where early diagnosis is important. Our aim was to present reference values for chest CT volumetric and radiodensity measurements and explore their potential in detecting early signs of CAL.MethodsFrom the population-based Swedish CArdioPulmonarybioImage Study (SCAPIS), 294 participants aged 50–64, were categorized into non-CAL (n = 258) and CAL (n = 36) groups based on spirometry. From inspiratory and expiratory CT images we compared lung volumes, mean lung density (MLD), percentage of low attenuation volume (LAV%) and LAV cluster volume between groups, and against reference values from static pulmonary function test (PFT).ResultsThe CAL group exhibited larger lung volumes, higher LAV%, increased LAV cluster volume and lower MLD compared to the non-CAL group. Lung volumes significantly deviated from PFT values. Expiratory measurements yielded more reliable results for identifying CAL compared to inspiratory. Using a cut-off value of 0.6 for expiratory LAV%, we achieved sensitivity, specificity and positive/negative predictive values of 72%, 85% and 40%/96%, respectively.ConclusionWe present volumetric reference values from inspiratory and expiratory chest CT images for a middle-aged healthy cohort. These results are not directly comparable to those from PFTs. Measures of MLD and LAV can be valuable in the evaluation of suspected CAL. Further validation and refinement are necessary to demonstrate its potential as a decision support tool for early detection of COPD.
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- Heil, Raphaela, et al.
(författare)
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A Study of Augmentation Methods for Handwritten Stenography Recognition
- 2023
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Konferensbidrag (refereegranskat)abstract
- One of the factors limiting the performance of handwritten text recognition (HTR) for stenography is the small amount of annotated training data. To alleviate the problem of data scarcity, modern HTR methods often employ data augmentation. However, due to specifics of the stenographic script, such settings may not be directly applicable for stenography recognition. In this work, we study 22 classical augmentation techniques, most of which are commonly used for HTR of other scripts, such as Latin handwriting. Through extensive experiments, we identify a group of augmentations, including for example contained ranges of random rotation, shifts and scaling, that are beneficial to the use case of stenography recognition. Furthermore, a number of augmentation approaches, leading to a decrease in recognition performance, are identified. Our results are supported by statistical hypothesis testing. A link to the source code is provided in the paper.
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