scholarly journals An Efficient Hybrid Fuzzy-Clustering Driven 3D-Modeling of Magnetic Resonance Imagery for Enhanced Brain Tumor Diagnosis

Electronics ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 475 ◽  
Author(s):  
Suresh Kanniappan ◽  
Duraimurugan Samiayya ◽  
Durai Raj Vincent P M ◽  
Kathiravan Srinivasan ◽  
Dushantha Nalin K. Jayakody ◽  
...  

Brain tumor detection and its analysis are essential in medical diagnosis. The proposed work focuses on segmenting abnormality of axial brain MR DICOM slices, as this format holds the advantage of conserving extensive metadata. The axial slices presume the left and right part of the brain is symmetric by a Line of Symmetry (LOS). A semi-automated system is designed to mine normal and abnormal structures from each brain MR slice in a DICOM study. In this work, Fuzzy clustering (FC) is applied to the DICOM slices to extract various clusters for different k. Then, the best-segmented image that has high inter-class rigidity is obtained using the silhouette fitness function. The clustered boundaries of the tissue classes further enhanced by morphological operations. The FC technique is hybridized with the standard image post-processing techniques such as marker controlled watershed segmentation (MCW), region growing (RG), and distance regularized level sets (DRLS). This procedure is implemented on renowned BRATS challenge dataset of different modalities and a clinical dataset containing axial T2 weighted MR images of a patient. The sequential analysis of the slices is performed using the metadata information present in the DICOM header. The validation of the segmentation procedures against the ground truth images authorizes that the segmented objects of DRLS through FC enhanced brain images attain maximum scores of Jaccard and Dice similarity coefficients. The average Jaccard and dice scores for segmenting tumor part for ten patient studies of the BRATS dataset are 0.79 and 0.88, also for the clinical study 0.78 and 0.86, respectively. Finally, 3D visualization and tumor volume estimation are done using accessible DICOM information.

2020 ◽  
Vol 64 (4) ◽  
pp. 40412-1-40412-11
Author(s):  
Kexin Bai ◽  
Qiang Li ◽  
Ching-Hsin Wang

Abstract To address the issues of the relatively small size of brain tumor image datasets, severe class imbalance, and low precision in existing segmentation algorithms for brain tumor images, this study proposes a two-stage segmentation algorithm integrating convolutional neural networks (CNNs) and conventional methods. Four modalities of the original magnetic resonance images were first preprocessed separately. Next, preliminary segmentation was performed using an improved U-Net CNN containing deep monitoring, residual structures, dense connection structures, and dense skip connections. The authors adopted a multiclass Dice loss function to deal with class imbalance and successfully prevented overfitting using data augmentation. The preliminary segmentation results subsequently served as the a priori knowledge for a continuous maximum flow algorithm for fine segmentation of target edges. Experiments revealed that the mean Dice similarity coefficients of the proposed algorithm in whole tumor, tumor core, and enhancing tumor segmentation were 0.9072, 0.8578, and 0.7837, respectively. The proposed algorithm presents higher accuracy and better stability in comparison with some of the more advanced segmentation algorithms for brain tumor images.


Author(s):  
Srinivasan A ◽  
Sudha S

One of the main causes of blindness is diabetic retinopathy (DR) and it may affect people of any ages. In these days, both young and old ages are affected by diabetes, and the di abetes is the main cause of DR. Hence, it is necessary to have an automated system with good accuracy and less computation time to diagnose and treat DR, and the automated system can simplify the work of ophthalmologists. The objective is to present an overview of various works recently in detecting and segmenting the various lesions of DR. Papers were categorized based on the diagnosing tools and the methods used for detecting early and advanced stage lesions. The early lesions of DR are microaneurysms, hemorrhages, exudates, and cotton wool spots and in the advanced stage, new and fragile blood vessels can be grown. Results have been evaluated in terms of sensitivity, specificity, accuracy and receiver operating characteristic curve. This paper analyzed the various steps and different algorithms used recently for the detection and classification of DR lesions. A comparison of performances has been made in terms of sensitivity, specificity, area under the curve, and accuracy. Suggestions, future workand the area to be improved were also discussed.Keywords: Diabetic retinopathy, Image processing, Morphological operations, Neural network, Fuzzy logic. 


2021 ◽  
Vol 4 ◽  
Author(s):  
Rolando Coto-Solano ◽  
James N. Stanford ◽  
Sravana K. Reddy

In recent decades, computational approaches to sociophonetic vowel analysis have been steadily increasing, and sociolinguists now frequently use semi-automated systems for phonetic alignment and vowel formant extraction, including FAVE (Forced Alignment and Vowel Extraction, Rosenfelder et al., 2011; Evanini et al., Proceedings of Interspeech, 2009), Penn Aligner (Yuan and Liberman, J. Acoust. Soc. America, 2008, 123, 3878), and DARLA (Dartmouth Linguistic Automation), (Reddy and Stanford, DARLA Dartmouth Linguistic Automation: Online Tools for Linguistic Research, 2015a). Yet these systems still have a major bottleneck: manual transcription. For most modern sociolinguistic vowel alignment and formant extraction, researchers must first create manual transcriptions. This human step is painstaking, time-consuming, and resource intensive. If this manual step could be replaced with completely automated methods, sociolinguists could potentially tap into vast datasets that have previously been unexplored, including legacy recordings that are underutilized due to lack of transcriptions. Moreover, if sociolinguists could quickly and accurately extract phonetic information from the millions of hours of new audio content posted on the Internet every day, a virtual ocean of speech from newly created podcasts, videos, live-streams, and other audio content would now inform research. How close are the current technological tools to achieving such groundbreaking changes for sociolinguistics? Prior work (Reddy et al., Proceedings of the North American Association for Computational Linguistics 2015 Conference, 2015b, 71–75) showed that an HMM-based Automated Speech Recognition system, trained with CMU Sphinx (Lamere et al., 2003), was accurate enough for DARLA to uncover evidence of the US Southern Vowel Shift without any human transcription. Even so, because that automatic speech recognition (ASR) system relied on a small training set, it produced numerous transcription errors. Six years have passed since that study, and since that time numerous end-to-end automatic speech recognition (ASR) algorithms have shown considerable improvement in transcription quality. One example of such a system is the RNN/CTC-based DeepSpeech from Mozilla (Hannun et al., 2014). (RNN stands for recurrent neural networks, the learning mechanism for DeepSpeech. CTC stands for connectionist temporal classification, the mechanism to merge phones into words). The present paper combines DeepSpeech with DARLA to push the technological envelope and determine how well contemporary ASR systems can perform in completely automated vowel analyses with sociolinguistic goals. Specifically, we used these techniques on audio recordings from 352 North American English speakers in the International Dialects of English Archive (IDEA1), extracting 88,500 tokens of vowels in stressed position from spontaneous, free speech passages. With this large dataset we conducted acoustic sociophonetic analyses of the Southern Vowel Shift and the Northern Cities Chain Shift in the North American IDEA speakers. We compared the results using three different sources of transcriptions: 1) IDEA’s manual transcriptions as the baseline “ground truth”, 2) the ASR built on CMU Sphinx used by Reddy et al. (Proceedings of the North American Association for Computational Linguistics 2015 Conference, 2015b, 71–75), and 3) the latest publicly available Mozilla DeepSpeech system. We input these three different transcriptions to DARLA, which automatically aligned and extracted the vowel formants from the 352 IDEA speakers. Our quantitative results show that newer ASR systems like DeepSpeech show considerable promise for sociolinguistic applications like DARLA. We found that DeepSpeech’s automated transcriptions had significantly fewer character error rates than those from the prior Sphinx system (from 46 to 35%). When we performed the sociolinguistic analysis of the extracted vowel formants from DARLA, we found that the automated transcriptions from DeepSpeech matched the results from the ground truth for the Southern Vowel Shift (SVS): five vowels showed a shift in both transcriptions, and two vowels didn’t show a shift in either transcription. The Northern Cities Shift (NCS) was more difficult to detect, but ground truth and DeepSpeech matched for four vowels: One of the vowels showed a clear shift, and three showed no shift in either transcription. Our study therefore shows how technology has made progress toward greater automation in vowel sociophonetics, while also showing what remains to be done. Our statistical modeling provides a quantified view of both the abilities and the limitations of a completely “hands-free” analysis of vowel shifts in a large dataset. Naturally, when comparing a completely automated system against a semi-automated system involving human manual work, there will always be a tradeoff between accuracy on the one hand versus speed and replicability on the other hand [Kendall and Joseph, Towards best practices in sociophonetics (with Marianna DiPaolo), 2014]. The amount of “noise” that can be tolerated for a given study will depend on the particular research goals and researchers’ preferences. Nonetheless, our study shows that, for certain large-scale applications and research goals, a completely automated approach using publicly available ASR can produce meaningful sociolinguistic results across large datasets, and these results can be generated quickly, efficiently, and with full replicability.


2018 ◽  
Vol 7 (3.1) ◽  
pp. 186
Author(s):  
Ramyasri Nayak ◽  
Nandish S ◽  
Prakashini Koteshwara

Many of the imaging modalities like X-ray, Computed Tomography (CT), Magnetic Resonance Imaging (MRI), fMRI have emerged to capture high quality images of anatomical structures of the human body. Radiologist can also have a better visualization if the regions of interest in the images are extracted and visualized 3D. To extract region of interest, sometimes preprocessing steps are performed on the input data. Pulmonary lesion is a small round or oval-shaped growth in the lung. It consists of solid and non-solid portion. The estimation of solid and non-solid portion of the pulmonary nodules will help the clinicians in the diagnosis and to suggest the appropriate treatment methodology. Lesion volume estimation gives a brief idea about the area occupied by the lesion tissues, which in turn can help the radiologist to plan treatment accordingly. In proposed work, lesion is segmented using K-means algorithm and then volume of the lesion is estimated. The slices which have segmented lesion with solid and non-solid regions is used for 3D visualization. The results obtained using the proposed methodology is validated with the Slicer 3D software. Error in the estimated volume of the solid and non-solid portion of the lesion was found to be in the range of 1.11% - 3.30% and 0.1% to 4.55% respectively. Results from the proposed methodology, lesion extraction with solid and non-solid, 3D visualization of the same and volume estimation respectively are validated by taking feedback from the radiologists and segmented lesion slices are used to estimate the volume and 3D visualization in Slicer 3D software for validation.  


2016 ◽  
Vol 153 (10) ◽  
pp. 41-49 ◽  
Author(s):  
Md. Sujan ◽  
Nashid Alam ◽  
Syed Abdullah ◽  
M. Jahirul

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi170-vi170 ◽  
Author(s):  
Siddhesh Thakur ◽  
Jimit Doshi ◽  
Sung Min Ha ◽  
Gaurav Shukla ◽  
Aikaterini Kotrotsou ◽  
...  

Abstract BACKGROUND Skull-stripping describes essential pre-processing in neuro-imaging, directly impacting subsequent analyses. Existing skull-stripping algorithms are typically developed and validated only on T1-weighted MRI scans without apparent gliomas, hence may fail when applied on neuro-oncology scans. Furthermore, most algorithms have large computational footprint and lack generalization to different acquisition protocols, limiting their clinical use. We sought to identify a practical, generalizable, robust, and accurate solution to address all these limitations. METHODS We identified multi-institutional retrospective cohorts, describing pre-operative multi-parametric MRI modalities (T1,T1Gd,T2,T2-FLAIR) with distinct acquisition protocols (e.g., slice thickness, magnet strength), varying pre-applied image-based defacing techniques, and corresponding manually-delineated ground-truth brain masks. We developed a 3D fully convolutional deep learning architecture (3D-ResUNet). Following modality co-registration to a common anatomical template, the 3D-ResUNet was trained on 314 subjects from the University of Pennsylvania (UPenn), and evaluated on 91, 152, 25, and 29 unseen subjects from UPenn, Thomas Jefferson University (TJU), Washington University (WashU), and MD Anderson (MDACC), respectively. To achieve robustness against scanner/resolution variability and utilize all modalities, we introduced a novel “modality-agnostic” training approach, which allows application of the trained model on any single modality, without requiring a pre-determined modality as input. We calculate the final brain mask for any test subject by applying our trained modality-agnostic 3D-ResUNet model on the modality with the highest resolution. RESULTS The average(±stdDev) dice similarity coefficients achieved for our novel modality-agnostic model were equal to 97.81%+0.8, 95.59%+2.0, 91.61%+1.9, and 96.05%+1.4 for the unseen data from UPenn, TJU, WashU, and MDACC, respectively. CONCLUSIONS Our novel modality-agnostic skull-stripping approach produces robust near-human performance, generalizes across acquisition protocols, image-based defacing techniques, without requiring pre-determined input modalities or depending on the availability of a specific modality. Such an approach can facilitate tool standardization for harmonized pre-processing of neuro-oncology scans for multi-institutional collaborations, enabling further data sharing and computational analyses.


2018 ◽  
Vol 10 (12) ◽  
pp. 1907 ◽  
Author(s):  
Luís Pádua ◽  
Pedro Marques ◽  
Jonáš Hruška ◽  
Telmo Adão ◽  
Emanuel Peres ◽  
...  

This study aimed to characterize vineyard vegetation thorough multi-temporal monitoring using a commercial low-cost rotary-wing unmanned aerial vehicle (UAV) equipped with a consumer-grade red/green/blue (RGB) sensor. Ground-truth data and UAV-based imagery were acquired on nine distinct dates, covering the most significant vegetative growing cycle until harvesting season, over two selected vineyard plots. The acquired UAV-based imagery underwent photogrammetric processing resulting, per flight, in an orthophoto mosaic, used for vegetation estimation. Digital elevation models were used to compute crop surface models. By filtering vegetation within a given height-range, it was possible to separate grapevine vegetation from other vegetation present in a specific vineyard plot, enabling the estimation of grapevine area and volume. The results showed high accuracy in grapevine detection (94.40%) and low error in grapevine volume estimation (root mean square error of 0.13 m and correlation coefficient of 0.78 for height estimation). The accuracy assessment showed that the proposed method based on UAV-based RGB imagery is effective and has potential to become an operational technique. The proposed method also allows the estimation of grapevine areas that can potentially benefit from canopy management operations.


Author(s):  
Ching-Lin Wang ◽  
Chi-Shiang Chan ◽  
Wei-Jyun Wang ◽  
Yung-Kuan Chan ◽  
Meng-Hsiun Tsai ◽  
...  

When treating a brain tumor, a doctor needs to know the site and the size of the tumor. Positron emission tomography (PET) can be effectively applied to diagnose such cancers based on the heightened glucose metabolism of early-stage cancer cells. The purpose of this research is to extract the regions of skull, brain tumor, and brain tissue from a series of PET brain images and then a three-dimensional (3D) model is reconstructed from the extracted skulls, brain tumors, and brain tissues. Knowing the relative site and size of a tumor within the skull is helpful to a doctor. The contours obtained by the segmentation method proposed in this study are quantitatively compared with the contours drawn by doctors on the same image set since the ground truth is unknown. The experimental results are impressive.


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