This work tackles the automatic fine-grained slide quality assessment problem for digitized direct smears test using the Gram staining protocol. Automatic quality assessment can provide useful information for the pathologists and the whole digital pathology workflow. For instance, if the system found a slide to have a low staining quality, it could send a request to the automatic slide preparation system to remake the slide. If the system detects severe damage in the slides, it could notify the experts that manual microscope reading may be required. In order to address the quality assessment problem, we propose a deep neural network based framework to automatically assess the slide quality in a semantic way. Specifically, the first step of our framework is to perform dense fine-grained region classification on the whole slide and calculate the region histogram of the label distributions. Next, our framework will generate assessments of the slide quality from various perspectives: staining quality, information density, damage level and which regions are more valuable for subsequent high-magnification analysis. To make the information more accessible, we present our results in the form of a heat map and text summaries. Additionally, in order to stimulate research in this direction, we propose a novel dataset for slide quality assessment. Experiments show that the proposed framework outperforms recent related works.
In the scope of Gram stain test, most related works @cite_30 @cite_14 @cite_15 only aim to detect and count the existence of different cells and bacteria. Despite the fact that progress has been made, these works assume that the areas of interest have been pre-selected by experts. As such, the fast automatic area of interest selection @cite_22 in low magnitude objectives is becoming an important step to have a fully automated CAD system for this application. The reason is that the final analysis is done by using high-powered objectives (e.g. 100x) which involves extremely long scanning times, huge image storage, and long processing times. So in the real scenario, it is a common strategy to choose a subset of good regions in low-mag to zoom into for further high-mag analysis.
@cite_30 @cite_15 @cite_14 @cite_22
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Gram stained direct smears test is clinically useful in early identification of infections. Unfortunately, this practice is considered time consuming and labour intensive. Most existing effort in this area is to perform highmagnification analysis of images taken from manually selected areas. In this paper, we address the problem of the automatic selection of candidate areas (or patches) for subsequent high-magnification analysis. Specifically, we explore and study the possibility of selecting good working areas based on low-magnification images, where bacteria are likely to be found when viewed in high-magnification images. To this end, we develop an approach to classify the areas of interest according to the textural information of the image patch. We explore and study the efficacy of traditional textural features such as Histogram of Gradients, Local Binary Patterns, and 2 Dimensional Discrete Cosine Transform. Experiments show that the best variant method is able to select working areas where it is likely to find bacteria in high-powered objective images in a wide range of images. Microscope examination of Gram stained clinical specimens is used for aiding the diagnosis of patients with infectious diseases. In high volume pathology laboratories, this manual microscopy examination is considered time consuming and labour intensive. Unfortunately, despite the great benefits offered from the application of Computer Aided Diagnosis (CAD) systems, to our knowledge, the highest automation stage for Gram stained slide analysis is only at the pre-analytical process. This paper takes the first steps towards the application of computer vision to direct smear, Gram stained images. To that end, we present a novel Gram stain image dataset. In addition, we also propose a multiple covariance approach for leukocyte and epithelial cell detection in Gram stain images. Each covariance matrix represents a particular image region characterising the cell's deformed structure. As covariance matrices form points on an Symmetric Positive Definite (SPD) manifold, the traditional Euclidean-based analysis cannot be used. As such, we first map the manifold points into the Reproducing Kernel Hilbert Space (RKHS). The analysis is done via a novel kernel similarity function that allows comparison between sets of covariance matrices. The proposed approach is contrasted, in the proposed dataset, with two recent state of the art methods in pedestrian detection: Histogram Of Gradient (HOG) and the traditional single covariance matrix approach. We found that the proposed approach outperformed both of these methods. Abstract In many microscopy applications the images may contain both regions of low and high cell densities corresponding to different tissues or colonies at different stages of growth. This poses a challenge to most previously developed automated cell detection and counting methods, which are designed to handle either the low-density scenario (through cell detection) or the high-density scenario (through density estimation or texture analysis). The objective of this work is to detect all the instances of an object of interest in microscopy images. The instances may be partially overlapping and clustered. To this end we introduce a tree-structured discrete graphical model that is used to select and label a set of non-overlapping regions in the image by a global optimization of a classification score. Each region is labeled with the number of instances it contains – for example regions can be selected that contain two or three object instances, by defining separate classes for tuples of objects in the detection process. We show that this formulation can be learned within the structured output SVM framework and that the inference in such a model can be accomplished using dynamic programming on a tree structured region graph. Furthermore, the learning only requires weak annotations – a dot on each instance. The candidate regions for the selection are obtained as extremal region of a surface computed from the microscopy image, and we show that the performance of the model can be improved by considering a proxy problem for learning the surface that allows better selection of the extremal regions. Furthermore, we consider a number of variations for the loss function used in the structured output learning. The model is applied and evaluated over six quite disparate data sets of images covering: fluorescence microscopy, weak-fluorescence molecular images, phase contrast microscopy and histopathology images, and is shown to exceed the state of the art in performance. Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7 in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5 ) than either LDC (99.0 ) or LR (99.1 ) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98 . Discrimination of infection stage was less accurate, producing high specificity (99.8 ) but only 45.0 -66.8 sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection without staining or expert analysis.