| 1. |
- Bombrun, Maxime, et al.
(författare)
-
Decoding gene expression in 2D and 3D
- 2017
-
Ingår i: Image Analysis. - Cham : Springer. - 9783319591285 ; , s. 257-268
-
Konferensbidrag (refereegranskat)abstract
- Image-based sequencing of RNA molecules directly in tissue samples provides a unique way of relating spatially varying gene expression to tissue morphology. Despite the fact that tissue samples are typically cut in micrometer thin sections, modern molecular detection methods result in signals so densely packed that optical “slicing” by imaging at multiple focal planes becomes necessary to image all signals. Chromatic aberration, signal crosstalk and low signal to noise ratio further complicates the analysis of multiple sequences in parallel. Here a previous 2D analysis approach for image-based gene decoding was used to show how signal count as well as signal precision is increased when analyzing the data in 3D instead. We corrected the extracted signal measurements for signal crosstalk, and improved the results of both 2D and 3D analysis. We applied our methodologies on a tissue sample imaged in six fluorescent channels during five cycles and seven focal planes, resulting in 210 images. Our methods are able to detect more than 5000 signals representing 140 different expressed genes analyzed and decoded in parallel.
|
|
| 2. |
- Chowdhury, Manish, et al.
(författare)
-
Granulometry-based trabecular bone segmentation
- 2017
-
Ingår i: 20th Scandinavian Conference on Image Analysis, SCIA 2017. - Cham : Springer. - 9783319591285 ; , s. 100-108, s. 100-108
-
Konferensbidrag (refereegranskat)abstract
- The accuracy of the analyses for studying the three dimensional trabecular bone microstructure rely on the quality of the segmentation between trabecular bone and bone marrow. Such segmentation is challenging for images from computed tomography modalities that can be used in vivo due to their low contrast and resolution. For this purpose, we propose in this paper a granulometry-based segmentation method. In a first step, the trabecular thickness is estimated by using the granulometry in gray scale, which is generated by applying the opening morphological operation with ball-shaped structuring elements of different diameters. This process mimics the traditional sphere-fitting method used for estimating trabecular thickness in segmented images. The residual obtained after computing the granulometry is compared to the original gray scale value in order to obtain a measurement of how likely a voxel belongs to trabecular bone. A threshold is applied to obtain the final segmentation. Six histomorphometric parameters were computed on 14 segmented bone specimens imaged with cone-beam computed tomography (CBCT), considering micro-computed tomography (micro-CT) as the ground truth. Otsu’s thresholding and Automated Region Growing (ARG) segmentation methods were used for comparison. For three parameters (Tb.N, Tb.Th and BV/TV), the proposed segmentation algorithm yielded the highest correlations with micro-CT, while for the remaining three (Tb.Nd, Tb.Tm and Tb.Sp), its performance was comparable to ARG. The method also yielded the strongest average correlation (0.89). When Tb.Th was computed directly from the gray scale images, the correlation was superior to the binary-based methods. The results suggest that the proposed algorithm can be used for studying trabecular bone in vivo through CBCT.
|
|
| 3. |
- Hansen, Michael Adsetts Edberg, et al.
(författare)
-
State Estimation of the Performance of Gravity Tables Using Multispectral Image Analysis
- 2017
-
Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. - 9783319591285 ; 10270 LNCS, s. 471-480
-
Konferensbidrag (refereegranskat)abstract
- Gravity tables are important machinery that separate dense(healthy) grains from lighter (low yielding varieties) aiding in improving the overall quality of seed and grain processing. This paper aims at evaluating the operating states of such tables, which is a critical criterionrequired for the design and automation of the next generation of gravity separators. We present a method capable of detecting differences in grain densities, that as an elementary step forms the basis for a related optimization of gravity tables. The method is based on a multispectral imaging technology, capable of capturing differences in the surface chemistry of the kernels. The relevant micro-properties of the grains are estimated using a Canonical Discriminant Analysis (CDA) that segments the captured grains into individual kernels and we show that for wheat, our method correlates well with control measurements (R 2 = 0.93).
|
|
| 4. |
- Klintström, Benjamin, et al.
(författare)
-
Feature space clustering for trabecular bone segmentation
- 2017
-
Ingår i: 20th Scandinavian Conference on Image Analysis, SCIA 2017. - Cham : Springer. - 9783319591285 - 9783319591292 ; , s. 65-75
-
Konferensbidrag (refereegranskat)abstract
- Trabecular bone structure has been shown to impact bone strength and fracture risk. In vitro, this structure can be measured by micro-computed tomography (micro-CT). For clinical use, it would be valuable if multi-slice computed tomography (MSCT) could be used to analyse trabecular bone structure. One important step in the analysis is image volume segmentation. Previous segmentation techniques have either been computer resource intensive or produced sub-optimal results when used on MSCT data. This paper proposes a new segmentation method that tries to balance good results against computational complexity. Material. Fourteen human radius specimens where scanned with MSCT and segmented using the proposed method as well as two segmentation methods previously used to segment trabecular bone (Otsu and Automated Region Growing (ARG)). The proposed method (named FCH) uses a combination of feature space clustering, edge detection and hysteresis thresholding. For evaluation, we computed correlations with the reference method micro-CT for 7 structure parameters and measured segmentation time. Results. Correlations with micro-CT were highest for FCH in 3 cases, highest for ARG in 3 cases, and in general lower for Otsu. Both FCH and ARG had correlations higher than 0.80 for all parameters, except for trabecular thickness and trabecular termini. FCH was 60 times slower than Otsu, but 5 times faster than ARG. Discussion. The high correlations with micro-CT suggest that with a suitable segmentation method it might be possible to analyse trabecular bone structure using MSCT-machines. The proposed segmentation method may represent a useful balance between speed and accuracy.
|
|
| 5. |
- Larsson, Måns, 1989, et al.
(författare)
-
Max-margin learning of deep structured models for semantic segmentation
- 2017
-
Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. - 9783319591285 ; 10270 LNCS, s. 28-40
-
Konferensbidrag (refereegranskat)abstract
- During the last few years most work done on the task of image segmentation has been focused on deep learning and Convolutional Neural Networks (CNNs) in particular. CNNs are powerful for modeling complex connections between input and output data but lack the ability to directly model dependent output structures, for instance, enforcing properties such as smoothness and coherence. This drawback motivates the use of Conditional Random Fields (CRFs), widely applied as a post-processing step in semantic segmentation. In this paper, we propose a learning framework that jointly trains the parameters of a CNN paired with a CRF. For this, we develop theoretical tools making it possible to optimize a max-margin objective with back-propagation. The max-margin loss function gives the model good generalization capabilities. Thus, the method is especially suitable for applications where labelled data is limited, for example, medical applications. This generalization capability is reflected in our results where we are able to show good performance on two relatively small medical datasets. The method is also evaluated on a public benchmark (frequently used for semantic segmentation) yielding results competitive to state-of-the-art. Overall, we demonstrate that end-to-end max-margin training is preferred over piecewise training when combining a CNN with a CRF.
|
|
| 6. |
- Larsson, Måns, 1989, et al.
(författare)
-
Robust abdominal organ segmentation using regional convolutional neural networks
- 2017
-
Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. - 9783319591285 ; 10270 LNCS, s. 41-52
-
Konferensbidrag (refereegranskat)abstract
- A fully automatic system for abdominal organ segmentation is presented. As a first step, an organ localization is obtained via a robust and efficient feature registration method where the center of the organ is estimated together with a region of interest surrounding the center. Then, a convolutional neural network performing voxelwise classification is applied. The convolutional neural network consists of several full 3D convolutional layers and takes both low and high resolution image data as input, which is designed to ensure both local and global consistency. Despite limited training data, our experimental results are on par with state-of-the-art approaches that have been developed over many years. More specifically the method is applied to the MICCAI2015 challenge “Multi-Atlas Labeling Beyond the Cranial Vault” in the free competition for organ segmentation in the abdomen. It achieved the best results for 3 out of the 13 organs with a total mean Dice coefficient of 0.757 for all organs. Top scores were achieved for the gallbladder, the aorta and the right adrenal gland.
|
|
| 7. |
- Lidayová, Kristína, et al.
(författare)
-
Airway-tree segmentation in subjects with acute respiratory distress syndrome
- 2017
-
Ingår i: 20th Scandinavian Conference on Image Analysis, SCIA 2017. - Cham : Springer. - 9783319591285 ; , s. 76-87
-
Konferensbidrag (refereegranskat)abstract
- Acute respiratory distress syndrome (ARDS) is associated with a high mortality rate in intensive care units. To lower the number of fatal cases, it is necessary to customize the mechanical ventilator parameters according to the patient’s clinical condition. For this, lung segmentation is required to assess aeration and alveolar recruitment. Airway segmentation may be used to reach a more accurate lung segmentation. In this paper, we seek to improve lung segmentation results by proposing a novel automatic airway-tree segmentation that is able to address the heterogeneity of ARDS pathology by handling various lung intensities differently. The method detects a simplified airway skeleton, thereby obtains a set of seed points together with an approximate radius and intensity range related to each of the points. These seeds are the input for an onion-kernel region-growing segmentation algorithm where knowledge about radius and intensity range restricts the possible leakage in the parenchyma. The method was evaluated qualitatively on 70 thoracic Computed Tomography volumes of subjects with ARDS, acquired at significantly different mechanical ventilation conditions. It found a large proportion of airway branches including tiny poorly-aerated bronchi. Quantitative evaluation was performed indirectly and showed that the resulting airway segmentation provides important anatomic landmarks. Their correspondences are needed to help a registration-based segmentation of the lungs in difficult ARDS cases where the lung boundary contrast is completely missing. The proposed method takes an average time of 43 s to process a thoracic volume which is valuable for the clinical use.
|
|
| 8. |
- Suveer, Amit, et al.
(författare)
-
Enhancement of cilia sub-structures by multiple instance registration and super-resolution reconstruction
- 2017
-
Ingår i: Image Analysis. - Cham : Springer. - 9783319591285 ; , s. 362-374
-
Konferensbidrag (refereegranskat)abstract
- Ultrastructural analysis of cilia cross-sectional images using transmission electron microscopy (TEM) assists the pathologists to diagnose Primary Ciliary Dyskinesia, a genetic disease. The current diagnostic procedure is manual and difficult because of poor signal-to-noise ratio in TEM images. In this paper, we propose an automated multi-step registration approach to register many cilia cross-sectional instances. The novelty of the work is in the utilization of customized weight masks at each registration step to achieve good alignment of the specific cilium regions. Registration is followed by super-resolution reconstruction to enhance the substructural information. Landmarks matching based evaluation of registration results in pixel alignment error of 2.35±1.82" role="presentation">2.35±1.82 pixels, and the subjective analysis of super-resolution reconstructed cilium shows a clear improvement in the visibility of the substructures such as dynein arms, radial spokes, and central pair.
|
|
| 9. |
- Wang, Chunliang
(författare)
-
Segmentation of multiple structures in chest radiographs using multi-task fully convolutional networks
- 2017
-
Ingår i: 20th Scandinavian Conference on Image Analysis, SCIA 2017. - Cham : Springer. - 9783319591285 ; , s. 282-289
-
Konferensbidrag (refereegranskat)abstract
- Segmentation of various structures from the chest radiograph is often performed as an initial step in computer-aided diagnosis/detection (CAD) systems. In this study, we implemented a multi-task fully convolutional network (FCN) to simultaneously segment multiple anatomical structures, namely the lung fields, the heart, and the clavicles, in standard posterior-anterior chest radiographs. This is done by adding multiple fully connected output nodes on top of a single FCN and using different objective functions for different structures, rather than training multiple FCNs or using a single FCN with a combined objective function for multiple classes. In our preliminary experiments, we found that the proposed multi-task FCN can not only reduce the training and running time compared to treating the multi-structure segmentation problems separately, but also help the deep neural network to converge faster and deliver better segmentation results on some challenging structures, like the clavicle. The proposed method was tested on a public database of 247 posterior–anterior chest radiograph and achieved comparable or higher accuracy on most of the structures when compared with the state-of-the-art segmentation methods.
|
|
