Quantification of microscopy time-series of in vitro reconstituted motor driven microtubule (MT) transport in 'gliding assays' is typically performed using computational object tracking tools. However, these are limited to non-intersecting and rod-like filaments. Here, we describe a novel computational image-analysis pipeline, KnotResolver, to track image time-series of highly curved self-intersecting looped filaments (knots) by resolving cross-overs. The code integrates filament segmentation and cross-over or 'knot' identification based on directed graph representation, where nodes represent cross-overs and edges represent the path connecting them. The graphs are mapped back to contours and the distance to a reference minimized. We demonstrate the utility of the tool by segmentation and tracking MTs from experiments with dynein-driven wave like filament looping. The accuracy of contour detection is sub-pixel accuracy, and Dice scores indicate a robustness to noise, better than currently used tools. Thus KnotResolver overcomes multiple limitations of widely used tools in microscopy of cytoskeletal filament-like structures.
The context of this paper is the creation of large uniform archaeological datasets from heterogeneous published resources, such as find catalogues - with the help of AI and Big Data. The paper is concerned with the challenge of consistent assemblages of archaeological data. We cannot simply combine existing records, as they differ in terms of quality and recording standards. Thus, records have to be recreated from published archaeological illustrations. This is only a viable path with the help of automation. The contribution of this paper is a new workflow for collecting data from archaeological find catalogues available as legacy resources, such as archaeological drawings and photographs in large unsorted PDF files; the workflow relies on custom software (AutArch) supporting image processing, object detection, and interactive means of validating and adjusting automatically retrieved data. We integrate artificial intelligence (AI) in terms of neural networks for object detection and classification into the workflow, thereby speeding up, automating, and standardising data collection. Objects commonly found in archaeological catalogues - such as graves, skeletons, ceramics, ornaments, stone tools and maps - are detected. Those objects are spatially related and analysed to extract real-life attributes, such as the size and orientation of graves based on the north arrow and the scale. We also automate recording of geometric whole-outlines through contour detection, as an alternative to landmark-based geometric morphometrics. Detected objects, contours, and other automatically retrieved data can be manually validated and adjusted. We use third millennium BC Europe (encompassing cultures such as 'Corded Ware' and 'Bell Beaker', and their burial practices) as a 'testing ground' and for evaluation purposes; this includes a user study for the workflow and the AutArch software.
Most high-level computer vision tasks rely on low-level image operations as their initial processes. Operations such as edge detection, image enhancement, and super-resolution, provide the foundations for higher level image analysis. In this work we address the edge detection considering three main objectives: simplicity, efficiency, and generalization since current state-of-the-art (SOTA) edge detection models are increased in complexity for better accuracy. To achieve this, we present Tiny and Efficient Edge Detector (TEED), a light convolutional neural network with only $58K$ parameters, less than $0.2$% of the state-of-the-art models. Training on the BIPED dataset takes $less than 30 minutes$, with each epoch requiring $less than 5 minutes$. Our proposed model is easy to train and it quickly converges within very first few epochs, while the predicted edge-maps are crisp and of high quality. Additionally, we propose a new dataset to test the generalization of edge detection, which comprises samples from popular images used in edge detection and image segmentation. The source code is available in https://github.com/xavysp/TEED.
Crowd counting is a fundamental problem in crowd analysis which is typically accomplished by estimating a crowd density map and summing over the density values. However, this approach suffers from background noise accumulation and loss of density due to the use of broad Gaussian kernels to create the ground truth density maps. This issue can be overcome by narrowing the Gaussian kernel. However, existing approaches perform poorly when trained with ground truth density maps with broad kernels. To deal with this limitation, we propose using conditional diffusion models to predict density maps, as diffusion models show high fidelity to training data during generation. With that, we present $CrowdDiff$ that generates the crowd density map as a reverse diffusion process. Furthermore, as the intermediate time steps of the diffusion process are noisy, we incorporate a regression branch for direct crowd estimation only during training to improve the feature learning. In addition, owing to the stochastic nature of the diffusion model, we introduce producing multiple density maps to improve the counting performance contrary to the existing crowd counting pipelines. We conduct extensive experiments on publicly available datasets to validate the effectiveness of our method. $CrowdDiff$ outperforms existing state-of-the-art crowd counting methods on several public crowd analysis benchmarks with significant improvements.
Diabetic Retinopathy (DR) is a complication of long-standing, unchecked diabetes and one of the leading causes of blindness in the world. This paper focuses on improved and robust methods to extract some of the features of DR, viz. Blood Vessels and Exudates. Blood vessels are segmented using multiple morphological and thresholding operations. For the segmentation of exudates, k-means clustering and contour detection on the original images are used. Extensive noise reduction is performed to remove false positives from the vessel segmentation algorithm's results. The localization of Optic Disc using k-means clustering and template matching is also performed. Lastly, this paper presents a Deep Convolutional Neural Network (DCNN) model with 14 Convolutional Layers and 2 Fully Connected Layers, for the automatic, binary diagnosis of DR. The vessel segmentation, optic disc localization and DCNN achieve accuracies of 95.93%, 98.77% and 75.73% respectively. The source code and pre-trained model are available https://github.com/Sohambasu07/DR_2021
The goal of the Mars Sample Return campaign is to collect soil samples from the surface of Mars and return them to Earth for further study. The samples will be acquired and stored in metal tubes by the Perseverance rover and deposited on the Martian surface. As part of this campaign, it is expected that the Sample Fetch Rover will be in charge of localizing and gathering up to 35 sample tubes over 150 Martian sols. Autonomous capabilities are critical for the success of the overall campaign and for the Sample Fetch Rover in particular. This work proposes a novel system architecture for the autonomous detection and pose estimation of the sample tubes. For the detection stage, a Deep Neural Network and transfer learning from a synthetic dataset are proposed. The dataset is created from photorealistic 3D simulations of Martian scenarios. Additionally, the sample tubes poses are estimated using Computer Vision techniques such as contour detection and line fitting on the detected area. Finally, laboratory tests of the Sample Localization procedure are performed using the ExoMars Testing Rover on a Mars-like testbed. These tests validate the proposed approach in different hardware architectures, providing promising results related to the sample detection and pose estimation.
This work focuses on a parameter-free joint piecewise smooth image denoising and contour detection. Formulated as the minimization of a discrete Mumford-Shah functional and estimated via a theoretically grounded alternating minimization scheme, the bottleneck of such a variational approach lies in the need to fine-tune their hyperparameters, while not having access to ground truth data. To that aim, a Stein-like strategy providing optimal hyperparameters is designed, based on the minimization of an unbiased estimate of the quadratic risk. Efficient and automated minimization of the estimate of the risk crucially relies on an unbiased estimate of the gradient of the risk with respect to hyperparameters. Its practical implementation is performed using a forward differentiation of the alternating scheme minimizing the Mumford-Shah functional, requiring exact differentiation of the proximity operators involved. Intensive numerical experiments are performed on synthetic images with different geometry and noise levels, assessing the accuracy and the robustness of the proposed procedure. The resulting parameter-free piecewise-smooth estimation and contour detection procedure, not requiring prior image processing expertise nor annotated data, can then be applied to real-world images.
This paper presents the final results of the ICDAR 2021 Competition on Historical Map Segmentation (MapSeg), encouraging research on a series of historical atlases of Paris, France, drawn at 1/5000 scale between 1894 and 1937. The competition featured three tasks, awarded separately. Task~1 consists in detecting building blocks and was won by the L3IRIS team using a DenseNet-121 network trained in a weakly supervised fashion. This task is evaluated on 3 large images containing hundreds of shapes to detect. Task~2 consists in segmenting map content from the larger map sheet, and was won by the UWB team using a U-Net-like FCN combined with a binarization method to increase detection edge accuracy. Task~3 consists in locating intersection points of geo-referencing lines, and was also won by the UWB team who used a dedicated pipeline combining binarization, line detection with Hough transform, candidate filtering, and template matching for intersection refinement. Tasks~2 and~3 are evaluated on 95 map sheets with complex content. Dataset, evaluation tools and results are available under permissive licensing at \url{https://icdar21-mapseg.github.io/}.
Many edge and contour detection algorithms give a soft-value as an output and the final binary map is commonly obtained by applying an optimal threshold. In this paper, we propose a novel method to detect image contours from the extracted edge segments of other algorithms. Our method is based on an undirected graphical model with the edge segments set as the vertices. The proposed energy functions are inspired by the surround modulation in the primary visual cortex that help suppressing texture noise. Our algorithm can improve extracting the binary map, because it considers other important factors such as connectivity, smoothness, and length of the contour beside the soft-values. Our quantitative and qualitative experimental results show the efficacy of the proposed method.
Image segmentation is a primary task in many medical applications. Recently, many deep networks derived from U-Net have been extensively used in various medical image segmentation tasks. However, in most of the cases, networks similar to U-net produce coarse and non-smooth segmentations with lots of discontinuities. To improve and refine the performance of U-Net like networks, we propose the use of parallel decoders which along with performing the mask predictions also perform contour prediction and distance map estimation. The contour and distance map aid in ensuring smoothness in the segmentation predictions. To facilitate joint training of three tasks, we propose a novel architecture called Psi-Net with a single encoder and three parallel decoders (thus having a shape of $\Psi$), one decoder to learns the segmentation mask prediction and other two decoders to learn the auxiliary tasks of contour detection and distance map estimation. The learning of these auxiliary tasks helps in capturing the shape and the boundary information. We also propose a new joint loss function for the proposed architecture. The loss function consists of a weighted combination of Negative Log likelihood and Mean Square Error loss. We have used two publicly available datasets: 1) Origa dataset for the task of optic cup and disc segmentation and 2) Endovis segment dataset for the task of polyp segmentation to evaluate our model. We have conducted extensive experiments using our network to show our model gives better results in terms of segmentation, boundary and shape metrics.
Progress in deep learning has spawned great successes in many engineering applications. As a prime example, convolutional neural networks, a type of feedforward neural networks, are now approaching -- and sometimes even surpassing -- human accuracy on a variety of visual recognition tasks. Here, however, we show that these neural networks and their recent extensions struggle in recognition tasks where co-dependent visual features must be detected over long spatial ranges. We introduce the horizontal gated-recurrent unit (hGRU) to learn intrinsic horizontal connections -- both within and across feature columns. We demonstrate that a single hGRU layer matches or outperforms all tested feedforward hierarchical baselines including state-of-the-art architectures which have orders of magnitude more free parameters. We further discuss the biological plausibility of the hGRU in comparison to anatomical data from the visual cortex as well as human behavioral data on a classic contour detection task.