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Electron microscopy (EM) allows the identification of intracellular organelles such as mitochondria, providing insights for clinical and scientific studies. In recent years, a number of novel deep learning architectures have been published reporting superior performance, or even human-level accuracy, compared to previous approaches on public mitochondria segmentation datasets. Unfortunately, many of these publications do not make neither the code nor the full training details public to support the results obtained, leading to reproducibility issues and dubious model comparisons. For that reason, and following a recent code of best practices for reporting experimental results, we present an extensive study of the state-of-the-art deep learning architectures for the segmentation of mitochondria on EM volumes, and evaluate the impact in performance of different variations of 2D and 3D U-Net-like models for this task. To better understand the contribution of each component, a common set of pre- and post-processing operations has been implemented and tested with each approach. Moreover, an exhaustive sweep of hyperparameters values for all architectures have been performed and each configuration has been run multiple times to report the mean and standard deviation values of the evaluation metrics. Using this methodology, we found very stable architectures and hyperparameter configurations that consistently obtain state-of-the-art results in the well-known EPFL Hippocampus mitochondria segmentation dataset. Furthermore, we have benchmarked our proposed models on two other available datasets, Lucchi++ and Kasthuri++, where they outperform all previous works. The code derived from this research and its documentation are publicly available.

Accurate insect pest recognition is significant to protect the crop or take the early treatment on the infected yield, and it helps reduce the loss for the agriculture economy. Design an automatic pest recognition system is necessary because manual recognition is slow, time-consuming, and expensive. The Image-based pest classifier using the traditional computer vision method is not efficient due to the complexity. Insect pest classification is a difficult task because of various kinds, scales, shapes, complex backgrounds in the field, and high appearance similarity among insect species. With the rapid development of deep learning technology, the CNN-based method is the best way to develop a fast and accurate insect pest classifier. We present different convolutional neural network-based models in this work, including attention, feature pyramid, and fine-grained models. We evaluate our methods on two public datasets: the large-scale insect pest dataset, the IP102 benchmark dataset, and a smaller dataset, namely D0 in terms of the macro-average precision (MPre), the macro-average recall (MRec), the macro-average F1- score (MF1), the accuracy (Acc), and the geometric mean (GM). The experimental results show that combining these convolutional neural network-based models can better perform than the state-of-the-art methods on these two datasets. For instance, the highest accuracy we obtained on IP102 and D0 is $74.13\%$ and $99.78\%$, respectively, bypassing the corresponding state-of-the-art accuracy: $67.1\%$ (IP102) and $98.8\%$ (D0). We also publish our codes for contributing to the current research related to the insect pest classification problem.

Distance metric learning based on triplet loss has been applied with success in a wide range of applications such as face recognition, image retrieval, speaker change detection and recently recommendation with the CML model. However, as we show in this article, CML requires large batches to work reasonably well because of a too simplistic uniform negative sampling strategy for selecting triplets. Due to memory limitations, this makes it difficult to scale in high-dimensional scenarios. To alleviate this problem, we propose here a 2-stage negative sampling strategy which finds triplets that are highly informative for learning. Our strategy allows CML to work effectively in terms of accuracy and popularity bias, even when the batch size is an order of magnitude smaller than what would be needed with the default uniform sampling. We demonstrate the suitability of the proposed strategy for recommendation and exhibit consistent positive results across various datasets.

Accurate segmentation of the prostate from magnetic resonance (MR) images provides useful information for prostate cancer diagnosis and treatment. However, automated prostate segmentation from 3D MR images still faces several challenges. For instance, a lack of clear edge between the prostate and other anatomical structures makes it challenging to accurately extract the boundaries. The complex background texture and large variation in size, shape and intensity distribution of the prostate itself make segmentation even further complicated. With deep learning, especially convolutional neural networks (CNNs), emerging as commonly used methods for medical image segmentation, the difficulty in obtaining large number of annotated medical images for training CNNs has become much more pronounced that ever before. Since large-scale dataset is one of the critical components for the success of deep learning, lack of sufficient training data makes it difficult to fully train complex CNNs. To tackle the above challenges, in this paper, we propose a boundary-weighted domain adaptive neural network (BOWDA-Net). To make the network more sensitive to the boundaries during segmentation, a boundary-weighted segmentation loss (BWL) is proposed. Furthermore, an advanced boundary-weighted transfer leaning approach is introduced to address the problem of small medical imaging datasets. We evaluate our proposed model on the publicly available MICCAI 2012 Prostate MR Image Segmentation (PROMISE12) challenge dataset. Our experimental results demonstrate that the proposed model is more sensitive to boundary information and outperformed other state-of-the-art methods.

Object detection in remote sensing, especially in aerial images, remains a challenging problem due to low image resolution, complex backgrounds, and variation of scale and angles of objects in images. In current implementations, multi-scale based and angle-based networks have been proposed and generate promising results with aerial image detection. In this paper, we propose a novel loss function, called Salience Biased Loss (SBL), for deep neural networks, which uses salience information of the input image to achieve improved performance for object detection. Our novel loss function treats training examples differently based on input complexity in order to avoid the over-contribution of easy cases in the training process. In our experiments, RetinaNet was trained with SBL to generate an one-stage detector, SBL-RetinaNet. SBL-RetinaNet is applied to the largest existing public aerial image dataset, DOTA. Experimental results show our proposed loss function with the RetinaNet architecture outperformed other state-of-art object detection models by at least 4.31 mAP, and RetinaNet by 2.26 mAP with the same inference speed of RetinaNet.

The low resolution of objects of interest in aerial images makes pedestrian detection and action detection extremely challenging tasks. Furthermore, using deep convolutional neural networks to process large images can be demanding in terms of computational requirements. In order to alleviate these challenges, we propose a two-step, yes and no question answering framework to find specific individuals doing one or multiple specific actions in aerial images. First, a deep object detector, Single Shot Multibox Detector (SSD), is used to generate object proposals from small aerial images. Second, another deep network, is used to learn a latent common sub-space which associates the high resolution aerial imagery and the pedestrian action labels that are provided by the human-based sources

In this paper, we focus on three problems in deep learning based medical image segmentation. Firstly, U-net, as a popular model for medical image segmentation, is difficult to train when convolutional layers increase even though a deeper network usually has a better generalization ability because of more learnable parameters. Secondly, the exponential ReLU (ELU), as an alternative of ReLU, is not much different from ReLU when the network of interest gets deep. Thirdly, the Dice loss, as one of the pervasive loss functions for medical image segmentation, is not effective when the prediction is close to ground truth and will cause oscillation during training. To address the aforementioned three problems, we propose and validate a deeper network that can fit medical image datasets that are usually small in the sample size. Meanwhile, we propose a new loss function to accelerate the learning process and a combination of different activation functions to improve the network performance. Our experimental results suggest that our network is comparable or superior to state-of-the-art methods.

Fully convolutional deep neural networks have been asserted to be fast and precise frameworks with great potential in image segmentation. One of the major challenges in utilizing such networks raises when data is unbalanced, which is common in many medical imaging applications such as lesion segmentation where lesion class voxels are often much lower in numbers than non-lesion voxels. A trained network with unbalanced data may make predictions with high precision and low recall, being severely biased towards the non-lesion class which is particularly undesired in medical applications where false negatives are actually more important than false positives. Various methods have been proposed to address this problem including two step training, sample re-weighting, balanced sampling, and similarity loss functions. In this paper we developed a patch-wise 3D densely connected network with an asymmetric loss function, where we used large overlapping image patches for intrinsic and extrinsic data augmentation, a patch selection algorithm, and a patch prediction fusion strategy based on B-spline weighted soft voting to take into account the uncertainty of prediction in patch borders. We applied this method to lesion segmentation based on the MSSEG 2016 and ISBI 2015 challenges, where we achieved average Dice similarity coefficient of 69.9% and 65.74%, respectively. In addition to the proposed loss, we trained our network with focal and generalized Dice loss functions. Significant improvement in $F_1$ and $F_2$ scores and the APR curve was achieved in test using the asymmetric similarity loss layer and our 3D patch prediction fusion. The asymmetric similarity loss based on $F_\beta$ scores generalizes the Dice similarity coefficient and can be effectively used with the patch-wise strategy developed here to train fully convolutional deep neural networks for highly unbalanced image segmentation.

One of the time-consuming routine work for a radiologist is to discern anatomical structures from tomographic images. For assisting radiologists, this paper develops an automatic segmentation method for pelvic magnetic resonance (MR) images. The task has three major challenges 1) A pelvic organ can have various sizes and shapes depending on the axial image, which requires local contexts to segment correctly. 2) Different organs often have quite similar appearance in MR images, which requires global context to segment. 3) The number of available annotated images are very small to use the latest segmentation algorithms. To address the challenges, we propose a novel convolutional neural network called Attention-Pyramid network (APNet) that effectively exploits both local and global contexts, in addition to a data-augmentation technique that is particularly effective for MR images. In order to evaluate our method, we construct fine-grained (50 pelvic organs) MR image segmentation dataset, and experimentally confirm the superior performance of our techniques over the state-of-the-art image segmentation methods.

We propose an Active Learning approach to image segmentation that exploits geometric priors to streamline the annotation process. We demonstrate this for both background-foreground and multi-class segmentation tasks in 2D images and 3D image volumes. Our approach combines geometric smoothness priors in the image space with more traditional uncertainty measures to estimate which pixels or voxels are most in need of annotation. For multi-class settings, we additionally introduce two novel criteria for uncertainty. In the 3D case, we use the resulting uncertainty measure to show the annotator voxels lying on the same planar patch, which makes batch annotation much easier than if they were randomly distributed in the volume. The planar patch is found using a branch-and-bound algorithm that finds a patch with the most informative instances. We evaluate our approach on Electron Microscopy and Magnetic Resonance image volumes, as well as on regular images of horses and faces. We demonstrate a substantial performance increase over state-of-the-art approaches.