A hierarchical refinement algorithm for fully automatic gridding in spotted DNA microarray image processing

Microarray images, which allow the analysis of hybridization expressions of genes, have been one of the most widely used high-throughput technologies with many different applications. Accurate and automatic microarray image analysis is very important since researchers trust the information provided in these experiments and construct conclusions based on the results produced by the software responsible in analyzing the hybridized arrays. Every microarray image contains thousands of spots, so how to do the spots finding in microarray images accurately and automatically is very meaningful. There are always some problems, such as rotation and distortion, in a microarray image caused by mechanical errors and/or optical errors in the system. All these problems will hinder "doi"ng analysis automatically. Early research has worked out several algorithms to deal with the rotation problem, but those algorithms can not handle microarray images with distortions. In this paper, we propose a robust spots finding method to deal with both rotation and/or distortion in microarray images. The proposed method provides automatic gridding and can handle a microarray image with different type of rotation (global or sub-array rotation) and optical distortions.

Deep learning has become the main way of the object detection task for autonomous vehicles. Meanwhile, this method typically requires vast amounts of training data to reach their full potential. However, collecting the data from real world and labeling manually is an expensive, time-consuming and error-prone process. Synthetic image has the potential to replace real image for training neural networks, because image creation and labeling annotations are free in this way. For the network trained by synthetic images, the reality gap between real and synthetic images is the main obstacle to use it in the real world. And most previous works are only devoted to generate synthetic images with a good performance on model training, but lack of analysis of the domain gap that affects the performance. This work designs a method of generating the real and synthetic images to analyze and reduce the reality gap between synthetic and real images for car detection. Firstly, this work put one single car with no-background in a random background image to generate real single car and synthetic single car images. In order to further reduce the domain gap in content level, this method keeps the car distribution in synthetic images is similar with the distribution of car in real world. For the purpose of reducing the domain gap in appearance level, the parameters of camera model are same as the camera parameters of image collecting cars and the image is rendered by using the PBRT(Physically Based Ray Tracing) when we generated the synthetic images. Secondly, by training the neural network of instance segmentation with different datasets, the across validation result proves that the reality gap between synthetic and real images is no more than the domain gap between real images. Thirdly, the training results of datasets with different samples diversity show that the diversity of the samples yields better generalization between different datasets for car detection which can effectively reduce the domain gap.

Gridding and spot segmentation are two critical steps in microarray gene expression data analysis. However, the problems of noise contamination and donut-shaped spots often make signal extraction process a laborintensive task. In this paper, we propose a three-step method for automatic gridding and spot segmentation. The method starts with a background removal and noise eliminating step, and then proceeds in two steps. The first step applies a fully unsupervised method to extract blocks and grids from the cleaned data. The second step applies a simple, progressive spot segmentation method to deal with inner holes and noise in spots. We tested its performance on real microarray images against a widely used software GenePix. Our results show that the proposed method deals effectively with poor-conditioned microarray images in both gridding and spot segmentation.

DNA microarray technology has permitted the analysis of global gene expression profiles in clinical diagnosis, treatment, and environmental health research for several diseases including cancer. Microarray images analysis, processing and segmentation are decisive steps in gene expression analysis, since any error leads to improper diagnosis. These techniques increased and enhanced over the past few years. However, the segmentation of the unshaped spots within the microarray image is still a problem due to the variations of spots in shapes and sizes. Hence, we introduce a new unshaped microarray spot segmentation model, which focuses on spots detection and segmentation regardless of their size and shape using fractal dimensions transform. Real microarray images from the Stanford Microarray Images Database (SMD) and Universal Microarray Images Database (UNC) are used to evaluate the efficiency of the proposed model. The numerical and visual results show that the proposed model improves the accuracy and the efficiency of the spots segmentation process. Biological researchers can use this model in their labs and clinics, as a free priceless software instead of using expensive ones like ScanAlyze, GenePix or spot software.

We consider the problem of object segmentation in cultural sites. Since collecting and labeling large datasets of real images is challenging, we investigate whether the use of synthetic images can be useful to achieve good segmentation performance on real data. To perform the study, we collected a new dataset comprising both real and synthetic images of 24 artworks in a cultural site. The synthetic images have been automatically generated from the 3D model of the considered cultural site using a tool developed for that purpose. Real and synthetic images have been labeled for the task of semantic segmentation of artworks. We compare three different approaches to perform object segmentation exploiting real and synthetic data. The experimental results point out that the use of synthetic data helps to improve the performances of segmentation algorithms when tested on real images. Satisfactory performance is achieved exploiting semantic segmentation together with image-to-image translation and including a small amount of real data during training. To encourage research on the topic, we publicly release the proposed dataset at the following url: https://iplab.dmi.unict.it/EGO-CH-OBJ-SEG/

Deep learning architectures can automatically learn complex features and patterns associated with glaucomatous optic neuropathy (GON). However, developing robust algorithms requires a large number of data sets. We sought to train an adversarial model for generating high-quality optic disc images from a large, diverse data set and then assessed the performance of models on generated synthetic images for detecting GON. A total of 17,060 (6874 glaucomatous and 10,186 healthy) fundus images were used to train deep convolutional generative adversarial networks (DCGANs) for synthesizing disc images for both classes. We then trained two models to detect GON, one solely on these synthetic images and another on a mixed data set (synthetic and real clinical images). Both the models were externally validated on a data set not used for training. The multiple classification metrics were evaluated with 95% confidence intervals. Models' decision-making processes were assessed using gradient-weighted class activation mapping (Grad-CAM) techniques. Following receiver operating characteristic curve analysis, an optimal cup-to-disc ratio threshold for detecting GON from the training data was found to be 0.619. DCGANs generated high-quality synthetic disc images for healthy and glaucomatous eyes. When trained on a mixed data set, the model's area under the receiver operating characteristic curve attained 99.85% on internal validation and 86.45% on external validation. Grad-CAM saliency maps were primarily centered on the optic nerve head, indicating a more precise and clinically relevant attention area of the fundus image. Although our model performed well on synthetic data, training on a mixed data set demonstrated better performance and generalization. Integrating synthetic and real clinical images can optimize the performance of a deep learning model in glaucoma detection. Optimizing deep learning models for glaucoma detection through integrating DCGAN-generated synthetic and real-world clinical data can be improved and generalized in clinical practice.

Microarray image processing plays an important role among array analysis and its precision will affect the application of gene chip. However, real microarray images drawn from various experimental procedures may contain noises and other artifacts, which result in a lower image processing accuracy. Hence, in this paper, we propose a novel image denoising method by introducing the compressed sensing theory into microarray image noise reduction. To improve the matching pursuit efficiency, the correlation coefficient is adopted. Experiments on 17 simulated images and 59 real microarray images obtained from the DeRisi, SIB and BCM data sets are conducted. Qualitative and quantitative results compared with the Donoho threshold, generalized wavelet and adaptive thresholding algorithm, reveal that our proposed method performs better on reducing the noises.

Digital twins (DT) offer a low-overhead evaluation platform and the ability to generate rich datasets for training machine learning (ML) models before actual deployment. Specifically, for the scenario of ML-aided millimeter wave (mmWave) links between moving vehicles to roadside units, we show how DT can create an accurate replica of the real world for model training and testing. The contributions of this paper are twofold: First, we propose a framework to create a multimodal Digital Twin (DT), where synthetic images and LiDAR data for the deployment location are generated along with RF propagation measurements obtained via ray-tracing. Second, to ensure effective domain adaptation, we leverage <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">meta-learning</i>, specifically <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Model-Agnostic Meta-Learning</i> (MAML), with <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">transfer learning</i> (TL) serving as a baseline validation approach. The proposed framework is validated using a comprehensive dataset containing both real and synthetic LiDAR and image data for mmWave V2X beam selection. It also enables the investigation of how each sensor modality impacts domain adaptation, taking into account the unique requirements of mmWave beam selection. Experimental results show that models trained on synthetic data using transfer learning and meta-learning, followed by minimal fine-tuning with real-world data, achieve up to 4.09× and 14.04× improvements in accuracy, respectively. These findings highlight the potential of synthetic data and meta-learning to bridge the domain gap and adapt rapidly to real-world beamforming challenges.

We present an Automatic License Plate Recognition system designed around Convolutional Neural Networks (CNNs) and trained over synthetic plate images. We first design CNNs suitable for plate and character detection, sharing a common architecture and training procedure. Then, we generate synthetic images that account for the varying illumination and pose conditions encountered with real plate images and we use exclusively such synthetic images to train our CNNs. Experiments with real vehicle images captured in natural light with commodity imaging systems show precision and recall in excess of 93% despite our networks are trained exclusively on synthetic images.

We present a diverse dataset of industrial metal objects with unique characteristics such as symmetry, texturelessness, and high reflectiveness. These features introduce challenging conditions that are not captured in existing datasets. Our dataset comprises both real-world and synthetic multi-view RGB images with 6D object pose labels. Real-world data were obtained by recording multi-view images of scenes with varying object shapes, materials, carriers, compositions, and lighting conditions. This resulted in over 30,000 real-world images. We introduce a new public tool that enables the quick annotation of 6D object pose labels in multi-view images. This tool was used to provide 6D object pose labels for all real-world images. Synthetic data were generated by carefully simulating real-world conditions and varying them in a controlled and realistic way. This resulted in over 500,000 synthetic images. The close correspondence between synthetic and real-world data and controlled variations will facilitate sim-to-real research. Our focus on industrial conditions and objects will facilitate research on computer vision tasks, such as 6D object pose estimation, which are relevant for many industrial applications, such as machine tending. The dataset and accompanying resources are available on the project website.

A microarray-image model is used that takes into account many factors, including spot morphology, signal strength, background fluorescent noise, and shape and surface degradation. The model yields synthetic images whose appearance and quality reflect that of real microarray images. The model is used to link noise factors to the fidelity of signal extraction with respect to a standard image-extraction algorithm. Of particular interest is the identification of the noise factors and their interactions that significantly degrade the ability to accurately detect the true gene-expression signal. This study uses statistical criteria in conjunction with the simulation of various noise conditions to better understand the noise influence on signal extraction for cDNA microarray images. It proposes a paradigm that is implemented in software. It specifically considers certain kinds of noise in the noise model and sets these at certain levels; however, one can choose other types of noise or use different noise levels. In sum, it develops a statistical package that can work in conjunction with the existing image simulation toolbox.

Recent advances in computer vision have shown promising results in image generation. Diffusion probabilistic models have generated realistic images from textual input, as demonstrated by DALL-E 2, Imagen, and Stable Diffusion. However, their use in medicine, where imaging data typically comprises three-dimensional volumes, has not been systematically evaluated. Synthetic images may play a crucial role in privacy-preserving artificial intelligence and can also be used to augment small datasets. We show that diffusion probabilistic models can synthesize high-quality medical data for magnetic resonance imaging (MRI) and computed tomography (CT). For quantitative evaluation, two radiologists rated the quality of the synthesized images regarding "realistic image appearance", "anatomical correctness", and "consistency between slices". Furthermore, we demonstrate that synthetic images can be used in self-supervised pre-training and improve the performance of breast segmentation models when data is scarce (Dice scores, 0.91 [without synthetic data], 0.95 [with synthetic data]).

Unmanned Aerial Vehicles are becoming increasingly popular for a broad variety of tasks ranging from aerial imagery to objects delivery. With the expansion of the areas, where drones can be efficiently used, the collision risk with other flying objects increases. Avoiding such collisions would be a relatively easy task, if all the aircrafts in the neighboring airspace could communicate with each other and share their location information. However, it is often the case that either location information is unavailable (e.g. flying in GPS-denied environments) or communication is not possible (e.g. different communication channels or non-cooperative flight scenario). To ensure flight safety in this kind of situations drones need a way to autonomously detect other objects that are intruding the neighboring airspace. Visual-based collision avoidance is of particular interest as cameras generally consume less power and are more lightweight than active sensor alternatives such as radars and lasers. We have therefore developed a set of increasingly sophisticated algorithms to provide drones with a visual collision avoidance capability. First, we present a novel method for detecting flying objects such as drones and planes that occupy a small part of the camera field of view, possibly move in front of complex backgrounds, and are filmed by a moving camera. In order to be solved this problem requires combining motion and appearance information, as neither of the two alone is capable of providing reliable enough detections. We therefore propose a machine learning technique that operates on spatio- temporal cubes of image intensities where individual patches are aligned using an object-centric regression-based motion stabilization algorithm. Second, in order to reduce the need to collect a large training dataset and to manual annotate it, we introduce a way to generate realistic synthetic images. Given only a small set of real examples and a coarse 3D model of the object, synthetic data can be generated in arbitrary quantities and further used to supplement real examples for training a detector. The key ingredient of our method is that the synthetically generated images need to be as close as possible to the real ones not in terms of image quality, but according to the features, used by a machine learning algorithm. Third, though the aforementioned approach yields a substantial increase in performance when using Adaboost and DPM detectors, it does not generalize well to Convolutional Neural Networks, which have become the state-of-the-art. This happens because, as we add more and more synthetic data, the CNNs begin to overfit to the synthetic images at the expense of the real ones. We therefore propose a novel deep domain adaptation technique that allows efficiently combining real and synthetic images without overfitting to either of the two. While most of the adaptation techniques aim at learning features that are invariant to the possible difference of the images, coming from different sources (real and synthetic). Unlike those methods, we suggest modeling this difference with a special two-stream architecture. We evaluate our approach on three different datasets and show its effectiveness for various classification and regression tasks.

Chest radiography is one of the most ubiquitous imaging modalities, playing an essential role in screening, diagnosis and disease management. However, chest radiography interpretation is a time-consuming and complex task, requiring the availability of experienced radiologists. As such, automated diagnosis systems for pathology detection have been proposed aiming to reduce the burden on radiologists and reduce variability in image interpretation. While promising results have been obtained, particularly since the advent of deep learning, there are significant limitations in the developed solutions, namely the lack of representative data for less frequent pathologies and the learning of biases from the training data, such as patient position, medical devices and other markers as proxies for certain pathologies. The lack of explainability is also a challenge for the adoption of these solutions in clinical practice.Generative adversarial networks could play a significant role as a solution for these challenges as they allow to artificially create new realistic images. This way, new synthetic chest radiography images could be used to increase the prevalence of less represented pathology classes and decrease model biases as well as improving the explainability of automatic decisions by generating samples that serve as examples or counter-examples to the image being analysed, ensuring patient privacy.In this study, a few-shot generative adversarial network is used to generate synthetic chest radiography images. A minimum Fréchet Inception Distance score of 17.83 was obtained, allowing to generate convincing synthetic images. Perceptual validation was then performed by asking multiple readers to classify a mixed set of synthetic and real images. An average accuracy of 83.5% was obtained but a strong dependency on reader experience level was observed. While synthetic images showed structural irregularities, the overall image sharpness was a major factor in the decision of readers. The synthetic images were then validated using a MobileNet abnormality classifier and it was shown that over 99% of images were classified correctly, indicating that the generated images were correctly interpreted by the classifier. Finally, the use of the synthetic images during training of a YOLOv5 pathology detector showed that the addition of the synthetic images led to an improvement of mean average precision of 0.05 across 14 pathologies.In conclusion, the usage of few-shot generative adversarial networks for chest radiography image generation was shown and tested in multiple scenarios, establishing a baseline for future experiments to increase the applicability of generative models in clinical scenarios of automatic CXR screening and diagnosis tools.

An unsupervised domain adaptation scheme for single-stage artwork recognition in cultural sites