2,281 research outputs found
Learning to Segment Microscopy Images with Lazy Labels
The need for labour intensive pixel-wise annotation is a major limitation of
many fully supervised learning methods for segmenting bioimages that can
contain numerous object instances with thin separations. In this paper, we
introduce a deep convolutional neural network for microscopy image
segmentation. Annotation issues are circumvented by letting the network being
trainable on coarse labels combined with only a very small number of images
with pixel-wise annotations. We call this new labelling strategy `lazy' labels.
Image segmentation is stratified into three connected tasks: rough inner region
detection, object separation and pixel-wise segmentation. These tasks are
learned in an end-to-end multi-task learning framework. The method is
demonstrated on two microscopy datasets, where we show that the model gives
accurate segmentation results even if exact boundary labels are missing for a
majority of annotated data. It brings more flexibility and efficiency for
training deep neural networks that are data hungry and is applicable to
biomedical images with poor contrast at the object boundaries or with diverse
textures and repeated patterns
Pseudo Mask Augmented Object Detection
In this work, we present a novel and effective framework to facilitate object
detection with the instance-level segmentation information that is only
supervised by bounding box annotation. Starting from the joint object detection
and instance segmentation network, we propose to recursively estimate the
pseudo ground-truth object masks from the instance-level object segmentation
network training, and then enhance the detection network with top-down
segmentation feedbacks. The pseudo ground truth mask and network parameters are
optimized alternatively to mutually benefit each other. To obtain the promising
pseudo masks in each iteration, we embed a graphical inference that
incorporates the low-level image appearance consistency and the bounding box
annotations to refine the segmentation masks predicted by the segmentation
network. Our approach progressively improves the object detection performance
by incorporating the detailed pixel-wise information learned from the
weakly-supervised segmentation network. Extensive evaluation on the detection
task in PASCAL VOC 2007 and 2012 [12] verifies that the proposed approach is
effective
Deep Interactive Region Segmentation and Captioning
With recent innovations in dense image captioning, it is now possible to
describe every object of the scene with a caption while objects are determined
by bounding boxes. However, interpretation of such an output is not trivial due
to the existence of many overlapping bounding boxes. Furthermore, in current
captioning frameworks, the user is not able to involve personal preferences to
exclude out of interest areas. In this paper, we propose a novel hybrid deep
learning architecture for interactive region segmentation and captioning where
the user is able to specify an arbitrary region of the image that should be
processed. To this end, a dedicated Fully Convolutional Network (FCN) named
Lyncean FCN (LFCN) is trained using our special training data to isolate the
User Intention Region (UIR) as the output of an efficient segmentation. In
parallel, a dense image captioning model is utilized to provide a wide variety
of captions for that region. Then, the UIR will be explained with the caption
of the best match bounding box. To the best of our knowledge, this is the first
work that provides such a comprehensive output. Our experiments show the
superiority of the proposed approach over state-of-the-art interactive
segmentation methods on several well-known datasets. In addition, replacement
of the bounding boxes with the result of the interactive segmentation leads to
a better understanding of the dense image captioning output as well as accuracy
enhancement for the object detection in terms of Intersection over Union (IoU).Comment: 17, pages, 9 figure
Segmentation Of Intracranial Structures From Noncontrast Ct Images With Deep Learning
Presented in this work is an investigation of the application of artificially intelligent algorithms, namely deep learning, to generate segmentations for the application in functional avoidance radiotherapy treatment planning. Specific applications of deep learning for functional avoidance include generating hippocampus segmentations from computed tomography (CT) images and generating synthetic pulmonary perfusion images from four-dimensional CT (4DCT).A single institution dataset of 390 patients treated with Gamma Knife stereotactic radiosurgery was created. From these patients, the hippocampus was manually segmented on the high-resolution MR image and used for the development of the data processing methodology and model testing. It was determined that an attention-gated 3D residual network performed the best, with 80.2% of contours meeting the clinical trial acceptability criteria. After having determined the highest performing model architecture, the model was tested on data from the RTOG-0933 Phase II multi-institutional clinical trial for hippocampal avoidance whole brain radiotherapy. From the RTOG-0933 data, an institutional observer (IO) generated contours to compare the deep learning style and the style of the physicians participating in the phase II trial. The deep learning model performance was compared with contour comparison and radiotherapy treatment planning. Results showed that the deep learning contours generated plans comparable to the IO style, but differed significantly from the phase II contours, indicating further investigation is required before this technology can be apply clinically. Additionally, motivated by the observed deviation in contouring styles of the trial’s participating treating physicians, the utility of applying deep learning as a first-pass quality assurance measure was investigated. To simulate a central review, the IO contours were compared to the treating physician contours in attempt to identify unacceptable deviations. The deep learning model was found to have an AUC of 0.80 for left, 0.79 for right hippocampus, thus indicating the potential applications of deep learning as a first-pass quality assurance tool. The methods developed during the hippocampal segmentation task were then translated to the generation of synthetic pulmonary perfusion imaging for use in functional lung avoidance radiotherapy. A clinical data set of 58 pre- and post-radiotherapy SPECT perfusion studies (32 patients) with contemporaneous 4DCT studies were collected. From the data set, 50 studies were used to train a 3D-residual network, with a five-fold validation used to select the highest performing model instances (N=5). The highest performing instances were tested on a 5 patient (8 study) hold-out test set. From these predictions, 50th percentile contours of well-perfused lung were generated and compared to contours from the clinical SPECT perfusion images. On the test set the Spearman correlation coefficient was strong (0.70, IQR: 0.61-0.76) and the functional avoidance contours agreed well Dice of 0.803 (IQR: 0.750-0.810), average surface distance of 5.92 mm (IQR: 5.68-7.55) mm. This study indicates the potential applications of deep learning for the generation of synthetic pulmonary perfusion images but requires an expanded dataset for additional model testing
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