manual segmentation
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2022 ◽  
Vol 2022 ◽  
pp. 1-10
Author(s):  
Zhenzhen Wang ◽  
Yating Mou ◽  
Hao Li ◽  
Rui Yang ◽  
Yanxun Jia

Cerebral haemorrhage is a serious subtype of stroke, with most patients experiencing short-term haematoma enlargement leading to worsening neurological symptoms and death. The main hemostatic agents currently used for cerebral haemorrhage are antifibrinolytics and recombinant coagulation factor VIIa. However, there is no clinical evidence that patients with cerebral haemorrhage can benefit from hemostatic treatment. We provide an overview of the mechanisms of haematoma expansion in cerebral haemorrhage and the progress of research on commonly used hemostatic drugs. To improve the semantic segmentation accuracy of cerebral haemorrhage, a segmentation method based on RGB-D images is proposed. Firstly, the parallax map was obtained based on a semiglobal stereo matching algorithm and fused with RGB images to form a four-channel RGB-D image to build a sample library. Secondly, the networks were trained with 2 different learning rate adjustment strategies for 2 different structures of convolutional neural networks. Finally, the trained networks were tested and compared for analysis. The 146 head CT images from the Chinese intracranial haemorrhage image database were divided into a training set and a test set using the random number table method. The validation set was divided into four methods: manual segmentation, algorithmic segmentation, the exact Tada formula, and the traditional Tada formula to measure the haematoma volume. The manual segmentation was used as the “gold standard,” and the other three algorithms were tested for consistency. The results showed that the algorithmic segmentation had the lowest percentage error of 15.54 (8.41, 23.18) % compared to the Tada formula method.


2022 ◽  
pp. 256-273
Author(s):  
Devidas Tulshiram Kushnure ◽  
Sanjay Nilkanth Talbar

Liver segmentation is instrumental for decision making in the medical realm for the diagnosis and treatment planning of hepatic diseases. However, the manual segmentation of the hundreds of CT images is tedious for medical experts. Thus, it hampers the segmentation accuracy and is reliant on opinion of the operator. This chapter presents the deep learning-based modified multi-scale UNet++ (M2UNet++) approach for automatic liver segmentation. The multi-scale features were modified channel-wise using adaptive feature recalibration to improve the representation of the high-level semantic information of the skip pathways and improved the segmentation performance with fewer computational overheads. The experimental results proved the model's efficacy on the publicly available 3DIRCADb dataset, which offers significant complexity and variations. The model's dice coefficient value is 97.28% that is 7.64%, and 2.24% improved from the UNet and UNet++ model. The quantitative result analysis shows that the M2UNet++ model outperforms the state-of-the-art methods proposed for liver segmentation.


2021 ◽  
Author(s):  
Andy Y. Wang ◽  
Vaishnavi Sharma ◽  
Harleen Saini ◽  
Joseph N. Tingen ◽  
Alexandra Flores ◽  
...  

ABSTRACTBackgroundWild-type transthyretin amyloidosis (ATTRwt) is an underdiagnosed and potentially fatal disease. Interestingly, ATTRwt deposits have been found to deposit in the ligamentum flavum (LF) of patients with lumbar spinal stenosis prior to the development of systemic and cardiac amyloidosis. In order to study this phenomenon and its possible relationship with LF thickening and systemic amyloidosis, a precise method of quantifying amyloid deposits in histological slides of LF is critical. However, such a method is currently unavailable. Here, we present a machine learning quantification method with Trainable Weka Segmentation (TWS) to assess amyloid deposition in histological slides of LF.MethodsImages of ligamentum flavum specimens stained with Congo red are obtained from spinal stenosis patients undergoing laminectomies and confirmed to be positive for ATTRwt. Amyloid deposits in these specimens are classified and quantified by TWS through training the algorithm via user-directed annotations on images of LF. TWS can also be automated through exposure to a set of training images with user-directed annotations, and then application to a set of new images without additional annotations. Additional methods of color thresholding and manual segmentation are also used on these images for comparison to TWS.ResultsWe develop the use of TWS in images of LF and demonstrate its potential for automated quantification. TWS is strongly correlated with manual segmentation in the training set of images with user-directed annotations (R = 0.98; p = 0.0033) as well as in the application set of images where TWS was automated (R = 0.94; p = 0.016). Color thresholding was weakly correlated with manual segmentation in the training set of images (R = 0.78; p = 0.12) and in the application set of images (R = 0.65; p = 0.23).ConclusionTWS machine learning closely correlates with the gold standard comparator of manual segmentation and outperforms the color thresholding method. This novel machine learning method to quantify amyloid deposition in histological slides of ligamentum flavum is a precise, objective, accessible, high throughput, and powerful tool that will hopefully pave the way towards future research and clinical applications.


Cancers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 5985
Author(s):  
Michelle Hershman ◽  
Bardia Yousefi ◽  
Lacey Serletti ◽  
Maya Galperin-Aizenberg ◽  
Leonid Roshkovan ◽  
...  

This study tackles interobserver variability with respect to specialty training in manual segmentation of non-small cell lung cancer (NSCLC). Four readers included for segmentation are: a data scientist (BY), a medical student (LS), a radiology trainee (MH), and a specialty-trained radiologist (SK) for a total of 295 patients from two publicly available databases. Sørensen–Dice (SD) coefficients and low rank Pearson correlation coefficients (CC) of 429 radiomics were calculated to assess interobserver variability. Cox proportional hazard (CPH) models and Kaplan-Meier (KM) curves of overall survival (OS) prediction for each dataset were also generated. SD and CC for segmentations demonstrated high similarities, yielding, SD: 0.79 and CC: 0.92 (BY-SK), SD: 0.81 and CC: 0.83 (LS-SK), and SD: 0.84 and CC: 0.91 (MH-SK) in average for both databases, respectively. OS through the maximal CPH model for the two datasets yielded c-statistics of 0.7 (95% CI) and 0.69 (95% CI), while adding radiomic and clinical variables (sex, stage/morphological status, and histology) together. KM curves also showed significant discrimination between high- and low-risk patients (p-value < 0.005). This supports that readers’ level of training and clinical experience may not significantly influence the ability to extract accurate radiomic features for NSCLC on CT. This potentially allows flexibility in the training required to produce robust prognostic imaging biomarkers for potential clinical translation.


2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Cheng-Hong Yang ◽  
Jai-Hong Ren ◽  
Hsiu-Chen Huang ◽  
Li-Yeh Chuang ◽  
Po-Yin Chang

Melanoma is a type of skin cancer that often leads to poor prognostic responses and survival rates. Melanoma usually develops in the limbs, including in fingers, palms, and the margins of the nails. When melanoma is detected early, surgical treatment may achieve a higher cure rate. The early diagnosis of melanoma depends on the manual segmentation of suspected lesions. However, manual segmentation can lead to problems, including misclassification and low efficiency. Therefore, it is essential to devise a method for automatic image segmentation that overcomes the aforementioned issues. In this study, an improved algorithm is proposed, termed EfficientUNet++, which is developed from the U-Net model. In EfficientUNet++, the pretrained EfficientNet model is added to the UNet++ model to accelerate segmentation process, leading to more reliable and precise results in skin cancer image segmentation. Two skin lesion datasets were used to compare the performance of the proposed EfficientUNet++ algorithm with other common models. In the PH2 dataset, EfficientUNet++ achieved a better Dice coefficient (93% vs. 76%–91%), Intersection over Union (IoU, 96% vs. 74%–95%), and loss value (30% vs. 44%–32%) compared with other models. In the International Skin Imaging Collaboration dataset, EfficientUNet++ obtained a similar Dice coefficient (96% vs. 94%–96%) but a better IoU (94% vs. 89%–93%) and loss value (11% vs. 13%–11%) than other models. In conclusion, the EfficientUNet++ model efficiently detects skin lesions by improving composite coefficients and structurally expanding the size of the convolution network. Moreover, the use of residual units deepens the network to further improve performance.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Varsha Alex ◽  
Tahmineh Motevasseli ◽  
William R. Freeman ◽  
Jefy A. Jayamon ◽  
Dirk-Uwe G. Bartsch ◽  
...  

AbstractComparing automated retinal layer segmentation using proprietary software (Heidelberg Spectralis HRA + OCT) and cross-platform Optical Coherence Tomography (OCT) segmentation software (Orion). Image segmentations of normal and diseased (iAMD, DME) eyes were performed using both softwares and then compared to the ‘gold standard’ of manual segmentation. A qualitative assessment and quantitative (layer volume) comparison of segmentations were performed. Segmented images from the two softwares were graded by two masked graders and in cases with difference, a senior retina specialist made a final independent decisive grading. Cross-platform software was significantly better than the proprietary software in the segmentation of NFL and INL layers in Normal eyes. It generated significantly better segmentation only for NFL in iAMD and for INL and OPL layers in DME eyes. In normal eyes, all retinal layer volumes calculated by the two softwares were moderate-strongly correlated except OUTLY. In iAMD eyes, GCIPL, INL, ONL, INLY, TRV layer volumes were moderate-strongly correlated between softwares. In eyes with DME, all layer volume values were moderate-strongly correlated between softwares. Cross-platform software can be used reliably in research settings to study the retinal layers as it compares well against manual segmentation and the commonly used proprietary software for both normal and diseased eyes.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 4633-4633
Author(s):  
Alice Motovylyak ◽  
Merryl Lobo ◽  
Rohit Sood

Abstract Primary myelofibrosis (PM) is a chronic blood cancer which increases burden on the spleen to produce blood cells and results in palpable splenomegaly. In the clinic, splenomegaly is classified based on the distance between the spleen's lowest point and the left costal margin, however, this method is highly subjective and depends on the subject's position and respiration. Imaging techniques have the potential to provide accurate, reliable, and reproducible measurements of splenic volume (SV). In clinical trials assessing therapy response, an accepted imaging-based endpoint is ≥35% reduction in SV at week 24 from baseline as measured by Magnetic Resonance Imaging (MRI) or Computer Tomography (CT). A ≥25% increase in SV is typically considered progression. The most accurate method for volume assessment is manual segmentation, since the entire spleen boundary can be utilized for the volume calculation. This study compared two other volume estimation methods: ellipsoid method and a model proposed by Bezerra et al (AJR Am J Roentgenol. 2005). We compared the methods' performance in assessing treatment response or progression based on SV change from baseline to week 24. Imaging data from 30 participants were used in this study, predominantly acquired using MRI modality; CT was used as an alternative, when MRI was contraindicated. Scans from two timepoints per participant were used: baseline and 24 weeks after start of treatment. For the manual segmentation method, preliminary regions of interest were manually outlined on every imaging slice by an experienced imaging analyst and then reviewed by a trained radiologist. SV was derived by multiplying the number of voxels contained in the spleen outlined by the voxel size of the scan. For the ellipsoid method, maximum width (W) and orthogonal thickness (T) were measured on the axial images. Length (L) was measured by multiplying the number of slices containing spleen by the slice interval. Ellipsoid volume was calculated as follows: V = W * T * L * π / 6 For the length-estimated SV based on the Bezerra et al model, spleen length was utilized as shown: V = (L - 5.8006) / 0.0126 For each of the three methods, percent change in SV was calculated from baseline to week 24. Pearson's correlation coefficient and Bland Altman analysis were implemented for comparison of methods to manual segmentation. Sensitivity and specificity analysis was performed to determine the accuracy of each method to predict response or progression. The manual segmentation volume was significantly correlated with both the ellipsoid method (r(58) = 0.94, p &lt; 0.0001) and the length-estimated method (r(58) = 0.89, p &lt; 0.0001). When assessing percent changes from baseline to week 24 using manual segmentation, 4 of the participants achieved splenic response and 4 progressed with 25% increase in SV. However, analysis using ellipsoid method yielded 3 responding and 2 progressing participants. Finally, analysis with length-estimated volume yielded no responding or progressing participants. This data is also illustrated in Table 1, which shows the sensitivity and specificity results. Figure 1 illustrates Bland-Altman plots, suggesting that ellipsoid method provides a more accurate estimation of the change in SV compared to length-estimated volume. Furthermore, we found that the inaccuracy with length-estimated volume increases with larger spleens (not shown). Change in spleen volume contributes to the primary/ secondary endpoints in large multi-center clinical trials for myelofibrosis, so it is imperative that the methods used to measure SV are consistent across imaging sites. The current standard for assessing SV is the manual segmentation method because it provides the most comprehensive measurement of spleen size however, this process is burdensome, time consuming, and requires specific training. The ellipsoid and length-estimated methods were strongly correlated with the manual segmentation method; however, they were not as sensitive when determining treatment response or progression. The length-estimated method had the least level of agreement with manual segmentation. The ellipsoid method may be a better alternative; however, it is important to use one method consistently across all visits for a study participant. Additional work is required to test performance of methods on a larger cohort, as well as assess automated segmentation algorithms that may reduce the burden of manual tracing. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.


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