The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in http://medicaldecathlon.com/. In addition, both data and online evaluation are accessible via https://competitions.codalab.org/competitions/17094

The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LITS) organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2016 and International Conference On Medical Image Computing Computer Assisted Intervention (MICCAI) 2017. Twenty four valid state-of-the-art liver and liver tumor segmentation algorithms were applied to a set of 131 computed tomography (CT) volumes with different types of tumor contrast levels (hyper-/hypo-intense), abnormalities in tissues (metastasectomie) size and varying amount of lesions. The submitted algorithms have been tested on 70 undisclosed volumes. The dataset is created in collaboration with seven hospitals and research institutions and manually reviewed by independent three radiologists. We found that not a single algorithm performed best for liver and tumors. The best liver segmentation algorithm achieved a Dice score of 0.96(MICCAI) whereas for tumor segmentation the best algorithm evaluated at 0.67(ISBI) and 0.70(MICCAI). The LITS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource.Comment: conferenc

The Importance of Skip Connections in Biomedical Image Segmentation

In this paper, we study the influence of both long and short skip connections on Fully Convolutional Networks (FCN) for biomedical image segmentation. In standard FCNs, only long skip connections are used to skip features from the contracting path to the expanding path in order to recover spatial information lost during downsampling. We extend FCNs by adding short skip connections, that are similar to the ones introduced in residual networks, in order to build very deep FCNs (of hundreds of layers). A review of the gradient flow confirms that for a very deep FCN it is beneficial to have both long and short skip connections. Finally, we show that a very deep FCN can achieve near-to-state-of-the-art results on the EM dataset without any further post-processing.Comment: Accepted to 2nd Workshop on Deep Learning in Medical Image Analysis (DLMIA 2016); Added reference

Live minimal path for interactive segmentation of medical images

Medical Imaging 2015: Image Processing, 94133U (20 mars 2015)Medical image segmentation is nowadays required for medical device development and in a growing number of clinical and research applications. Since dedicated automatic segmentation methods are not always available, generic and efficient interactive tools can alleviate the burden of manual segmentation. In this paper we propose an interactive segmentation tool based on image warping and minimal path segmentation that is efficient for a wide variety of segmentation tasks. While the user roughly delineates the desired organs boundary, a narrow band along the cursors path is straightened, providing an ideal subspace for feature aligned filtering and minimal path algorithm. Once the segmentation is performed on the narrow band, the path is warped back onto the original image, precisely delineating the desired structure. This tool was found to have a highly intuitive dynamic behavior. It is especially efficient against misleading edges and required only coarse interaction from the user to achieve good precision. The proposed segmentation method was tested for 10 difficult liver segmentations on CT and MRI images, and the resulting 2D overlap Dice coefficient was 99% on average

Liver segmentation on CT and MR using laplacian mesh optimization

Objective: The purpose of this paper is to describe a semiautomated segmentation method for the liver and evaluate its performance on CT-scan and MR images. Methods: First, an approximate 3-D model of the liver is initialized from a few user-generated contours to globally outline the liver shape. The model is then automatically deformed by a Laplacian mesh optimization scheme until it precisely delineates the patient’s liver. A correction tool was implemented to allow the user to improve the segmentation until satisfaction. Results: The proposed method was tested against 30 CT-scans from the SLIVER07 challenge repository and 20 MR studies from the Montreal University Hospital Center, covering a wide spectrum of liver morphologies and pathologies. The average volumetric overlap error was 5.1% for CT and 7.6% for MRI and the average segmentation time was 6 min. Conclusion: The obtained results show that the proposed method is efficient, reliable, and could effectively be used routinely in the clinical setting. Significance: The proposed approach can alleviate the cumbersome and tedious process of slice-wise segmentation required for precise hepatic volumetry, virtual surgery, and treatment planning

Liver Segmentation on CT and MR Using Laplacian Mesh Optimization

Objective: The purpose of this paper is to describe a semiautomated segmentation method for the liver and evaluate its performance on CT-scan and MR images. Methods: First, an approximate 3-D model of the liver is initialized from a few user-generated contours to globally outline the liver shape. The model is then automatically deformed by a Laplacian mesh optimization scheme until it precisely delineates the patient’s liver. A correction tool was implemented to allow the user to improve the segmentation until satisfaction. Results: The proposed method was tested against 30 CT-scans from the SLIVER07 challenge repository and 20 MR studies from the Montreal University Hospital Center, covering a wide spectrum of liver morphologies and pathologies. The average volumetric overlap error was 5.1% for CT and 7.6% for MRI and the average segmentation time was 6 min. Conclusion: The obtained results show that the proposed method is efficient, reliable, and could effectively be used routinely in the clinical setting. Significance: The proposed approach can alleviate the cumbersome and tedious process of slice-wise segmentation required for precise hepatic volumetry, virtual surgery, and treatment planning

Multi-isotopes in human hair: A tool to initiate cross-border collaboration in international cold-cases

Unidentified human remains have historically been investigated nationally by law enforcement authorities. However, this approach is outdated in a globalized world with rapid transportation means, where humans easily move long distances across borders. Cross-border cooperation in solving cold-cases is rare due to political, administrative or technical challenges. It is fundamental to develop new tools to provide rapid and cost-effective leads for international cooperation. In this work, we demonstrate that isotopic measurements are effective screening tools to help identify cold-cases with potential international ramifications. We first complete existing databases of hydrogen and sulfur isotopes in human hair from residents across North America by compiling or analyzing hair from Canada, the United States (US) and Mexico. Using these databases, we develop maps predicting isotope variations in human hair across North America. We demonstrate that both δ2H and δ34S values of human hair are highly predictable and display strong spatial patterns. Multi-isotope analysis combined with dual δ2H and δ34S geographic probability maps provide evidence for international travel in two case studies. In the first, we demonstrate that multi-isotope analysis in bulk hair of deceased border crossers found in the US, close to the Mexico-US border, help trace their last place of residence or travel back to specific regions of Mexico. These findings were validated by the subsequent identification of these individuals through the Pima County Office of the Medical Examiner in Tucson, Arizona. In the second case study, we demonstrate that sequential multi-isotope analysis along the hair strands of an unidentified individual found in Canada provides detailed insights into the international mobility of this individual during the last year of life. In both cases, isotope data provide strong leads towards international travel

Comparison of MRI - and CT-based semiautomated liver segmentation : a validation study

Purpose To compare the repeatability, agreement, and efficiency of MRI- and CT-based semiautomated liver segmentation for the assessment of total and subsegmental liver volume. Methods This retrospective study was conducted in 31 subjects who underwent contemporaneous liver MRI and CT. Total and subsegmental liver volumes were segmented from contrast-enhanced 3D gradient-recalled echo MRI sequences and CT images. Semiautomated segmentation was based on variational interpolation and Laplacian mesh optimization. All segmentations were repeated after 2 weeks. Manual segmentation of CT images using an active contour tool was used as the reference standard. Repeatability and agreement of the methods were evaluated with intra-class correlation coefficients (ICC) and Bland–Altman analysis. Total interaction time was recorded. Results Intra-reader ICC were ≥0.987 for MRI and ≥0.995 for CT. Intra-reader repeatability was 30 ± 217 ml (bias ± 1.96 SD) (95% limits of agreement: −187 to 247 ml) for MRI and −10 ± 143 ml (−153 to 133 ml) for CT. Inter-method ICC between semiautomated and manual volumetry were ≥0.995 for MRI and ≥0.986 for CT. Inter-method segmental ICC varied between 0.584 and 0.865 for MRI and between 0.596 and 0.890 for CT. Inter-method agreement was –14 ± 136 ml (−150 to 122 ml) for MRI and 50 ± 226 ml (−176 to 276 ml) for CT. Inter-method segmental agreement ranged from 10 ± 47 ml (−37 to 57 ml) to 2 ± 214 ml (−212 to 216 ml) for MRI and 9 ± 45 ml (−36 to 54 ml) to −46 ± 183 ml (−229 to 137 ml) for CT. Interaction time (mean ± SD) was significantly shorter for MRI-based semiautomated segmentation (7.2 ± 0.1 min, p < 0.001) and for CT-based semiautomated segmentation (6.5 ± 0.2 min, p < 0.001) than for CT-based manual segmentation (14.5 ± 0.4 min). Conclusion MRI-based semiautomated segmentation provides similar repeatability and agreement to CT-based segmentation for total liver volume