131 research outputs found
Prospects for Theranostics in Neurosurgical Imaging: Empowering Confocal Laser Endomicroscopy Diagnostics via Deep Learning
Confocal laser endomicroscopy (CLE) is an advanced optical fluorescence
imaging technology that has the potential to increase intraoperative precision,
extend resection, and tailor surgery for malignant invasive brain tumors
because of its subcellular dimension resolution. Despite its promising
diagnostic potential, interpreting the gray tone fluorescence images can be
difficult for untrained users. In this review, we provide a detailed
description of bioinformatical analysis methodology of CLE images that begins
to assist the neurosurgeon and pathologist to rapidly connect on-the-fly
intraoperative imaging, pathology, and surgical observation into a
conclusionary system within the concept of theranostics. We present an overview
and discuss deep learning models for automatic detection of the diagnostic CLE
images and discuss various training regimes and ensemble modeling effect on the
power of deep learning predictive models. Two major approaches reviewed in this
paper include the models that can automatically classify CLE images into
diagnostic/nondiagnostic, glioma/nonglioma, tumor/injury/normal categories and
models that can localize histological features on the CLE images using weakly
supervised methods. We also briefly review advances in the deep learning
approaches used for CLE image analysis in other organs. Significant advances in
speed and precision of automated diagnostic frame selection would augment the
diagnostic potential of CLE, improve operative workflow and integration into
brain tumor surgery. Such technology and bioinformatics analytics lend
themselves to improved precision, personalization, and theranostics in brain
tumor treatment.Comment: See the final version published in Frontiers in Oncology here:
https://www.frontiersin.org/articles/10.3389/fonc.2018.00240/ful
Radiomics analyses for outcome prediction in patients with locally advanced rectal cancer and glioblastoma multiforme using multimodal imaging data
Personalized treatment strategies for oncological patient management can improve outcomes of patient populations with heterogeneous treatment response. The implementation of such a concept requires the identification of biomarkers that can precisely predict treatment outcome. In the context of this thesis, we develop and validate biomarkers from multimodal imaging data for the outcome prediction after treatment in patients with locally advanced rectal cancer (LARC) and in patients with newly diagnosed glioblastoma multiforme (GBM), using conventional feature-based radiomics and deep-learning (DL) based radiomics. For LARC patients, we identify promising radiomics signatures combining computed tomography (CT) and T2-weighted (T2-w) magnetic resonance imaging (MRI) with clinical parameters to predict tumour response to neoadjuvant chemoradiotherapy (nCRT). Further, the analyses of externally available radiomics models for LARC reveal a lack of reproducibility and the need for standardization of the radiomics process. For patients with GBM, we use postoperative [11C] methionine positron emission tomography (MET-PET) and gadolinium-enhanced T1-w MRI for the detection of the residual tumour status and to prognosticate time-to-recurrence (TTR) and overall survival (OS). We show that DL models built on MET-PET have an improved diagnostic and prognostic value as compared to MRI
Impact of random outliers in auto-segmented targets on radiotherapy treatment plans for glioblastoma.
AIMS
To save time and have more consistent contours, fully automatic segmentation of targets and organs at risk (OAR) is a valuable asset in radiotherapy. Though current deep learning (DL) based models are on par with manual contouring, they are not perfect and typical errors, as false positives, occur frequently and unpredictably. While it is possible to solve this for OARs, it is far from straightforward for target structures. In order to tackle this problem, in this study, we analyzed the occurrence and the possible dose effects of automated delineation outliers.
METHODS
First, a set of controlled experiments on synthetically generated outliers on the CT of a glioblastoma (GBM) patient was performed. We analyzed the dosimetric impact on outliers with different location, shape, absolute size and relative size to the main target, resulting in 61 simulated scenarios. Second, multiple segmentation models where trained on a U-Net network based on 80 training sets consisting of GBM cases with annotated gross tumor volume (GTV) and edema structures. On 20 test cases, 5 different trained models and a majority voting method were used to predict the GTV and edema. The amount of outliers on the predictions were determined, as well as their size and distance from the actual target.
RESULTS
We found that plans containing outliers result in an increased dose to healthy brain tissue. The extent of the dose effect is dependent on the relative size, location and the distance to the main targets and involved OARs. Generally, the larger the absolute outlier volume and the distance to the target the higher the potential dose effect. For 120 predicted GTV and edema structures, we found 1887 outliers. After construction of the planning treatment volume (PTV), 137 outliers remained with a mean distance to the target of 38.5 ± 5.0 mm and a mean size of 1010.8 ± 95.6 mm3. We also found that majority voting of DL results is capable to reduce outliers.
CONCLUSIONS
This study shows that there is a severe risk of false positive outliers in current DL predictions of target structures. Additionally, these errors will have an evident detrimental impact on the dose and therefore could affect treatment outcome
Ensembles of Multiple Models and Architectures for Robust Brain Tumour Segmentation
Deep learning approaches such as convolutional neural nets have consistently
outperformed previous methods on challenging tasks such as dense, semantic
segmentation. However, the various proposed networks perform differently, with
behaviour largely influenced by architectural choices and training settings.
This paper explores Ensembles of Multiple Models and Architectures (EMMA) for
robust performance through aggregation of predictions from a wide range of
methods. The approach reduces the influence of the meta-parameters of
individual models and the risk of overfitting the configuration to a particular
database. EMMA can be seen as an unbiased, generic deep learning model which is
shown to yield excellent performance, winning the first position in the BRATS
2017 competition among 50+ participating teams.Comment: The method won the 1st-place in the Brain Tumour Segmentation (BRATS)
2017 competition (segmentation task
Uncertainty-driven refinement of tumor-core segmentation using 3D-to-2D networks with label uncertainty
The BraTS dataset contains a mixture of high-grade and low-grade gliomas,
which have a rather different appearance: previous studies have shown that
performance can be improved by separated training on low-grade gliomas (LGGs)
and high-grade gliomas (HGGs), but in practice this information is not
available at test time to decide which model to use. By contrast with HGGs,
LGGs often present no sharp boundary between the tumor core and the surrounding
edema, but rather a gradual reduction of tumor-cell density.
Utilizing our 3D-to-2D fully convolutional architecture, DeepSCAN, which
ranked highly in the 2019 BraTS challenge and was trained using an
uncertainty-aware loss, we separate cases into those with a confidently
segmented core, and those with a vaguely segmented or missing core. Since by
assumption every tumor has a core, we reduce the threshold for classification
of core tissue in those cases where the core, as segmented by the classifier,
is vaguely defined or missing.
We then predict survival of high-grade glioma patients using a fusion of
linear regression and random forest classification, based on age, number of
distinct tumor components, and number of distinct tumor cores.
We present results on the validation dataset of the Multimodal Brain Tumor
Segmentation Challenge 2020 (segmentation and uncertainty challenge), and on
the testing set, where the method achieved 4th place in Segmentation, 1st place
in uncertainty estimation, and 1st place in Survival prediction.Comment: Presented (virtually) in the MICCAI Brainles workshop 2020. Accepted
for publication in Brainles proceeding
'A net for everyone': fully personalized and unsupervised neural networks trained with longitudinal data from a single patient
With the rise in importance of personalized medicine, we trained personalized
neural networks to detect tumor progression in longitudinal datasets. The model
was evaluated on two datasets with a total of 64 scans from 32 patients
diagnosed with glioblastoma multiforme (GBM). Contrast-enhanced T1w sequences
of brain magnetic resonance imaging (MRI) images were used in this study. For
each patient, we trained their own neural network using just two images from
different timepoints. Our approach uses a Wasserstein-GAN (generative
adversarial network), an unsupervised network architecture, to map the
differences between the two images. Using this map, the change in tumor volume
can be evaluated. Due to the combination of data augmentation and the network
architecture, co-registration of the two images is not needed. Furthermore, we
do not rely on any additional training data, (manual) annotations or
pre-training neural networks. The model received an AUC-score of 0.87 for tumor
change. We also introduced a modified RANO criteria, for which an accuracy of
66% can be achieved. We show that using data from just one patient can be used
to train deep neural networks to monitor tumor change
- …