Automated Segmentation of Cells with IHC Membrane Staining

This study presents a fully automated membrane segmentation technique for immunohistochemical tissue images with membrane staining, which is a critical task in computerized immunohistochemistry (IHC). Membrane segmentation is particularly tricky in immunohistochemical tissue images because the cellular membranes are visible only in the stained tracts of the cell, while the unstained tracts are not visible. Our automated method provides accurate segmentation of the cellular membranes in the stained tracts and reconstructs the approximate location of the unstained tracts using nuclear membranes as a spatial reference. Accurate cell-by-cell membrane segmentation allows per cell morphological analysis and quantification of the target membrane proteins that is fundamental in several medical applications such as cancer characterization and classification, personalized therapy design, and for any other applications requiring cell morphology characterization. Experimental results on real datasets from different anatomical locations demonstrate the wide applicability and high accuracy of our approach in the context of IHC analysi

W2WNet: A two-module probabilistic Convolutional Neural Network with embedded data cleansing functionality

Ideally, Convolutional Neural Networks (CNNs) should be trained with high quality images with minimum noise and correct ground truth labels. Nonetheless, in many real-world scenarios, such high quality is very hard to obtain, and datasets may be affected by any sort of image degradation and mislabelling issues. This negatively impacts the performance of standard CNNs, both during the training and the inference phase. To address this issue we propose Wise2WipedNet (W2WNet), a new two-module Convolutional Neural Network, where a Wise module exploits Bayesian inference to identify and discard spurious images during the training and a Wiped module takes care of the final classification, while broadcasting information on the prediction confidence at inference time. The goodness of our solution is demonstrated on a number of public benchmarks addressing different image classification tasks, as well as on a real-world case study on histological image analysis. Overall, our experiments demonstrate that W2WNet is able to identify image degradation and mislabelling issues both at training and at inference time, with positive impact on the final classification accurac

W2WNet: a two-module probabilistic Convolutional Neural Network with embedded data cleansing functionality

Convolutional Neural Networks (CNNs) are supposed to be fed with only high-quality annotated datasets. Nonetheless, in many real-world scenarios, such high quality is very hard to obtain, and datasets may be affected by any sort of image degradation and mislabelling issues. This negatively impacts the performance of standard CNNs, both during the training and the inference phase. To address this issue we propose Wise2WipedNet (W2WNet), a new two-module Convolutional Neural Network, where a Wise module exploits Bayesian inference to identify and discard spurious images during the training, and a Wiped module takes care of the final classification while broadcasting information on the prediction confidence at inference time. The goodness of our solution is demonstrated on a number of public benchmarks addressing different image classification tasks, as well as on a real-world case study on histological image analysis. Overall, our experiments demonstrate that W2WNet is able to identify image degradation and mislabelling issues both at training and at inference time, with a positive impact on the final classification accuracy

Realistic Multi-Scale Modelling of Household Electricity Behaviours

To improve the management and reliability of power distribution networks, there is a strong demand for models simulating energy loads in a realistic way. In this paper, we present a novel multi-scale model to generate realistic residential load profiles at different spatial-temporal resolutions. By taking advantage of information from Census and national surveys, we generate statistically consistent populations of heterogeneous families with their respective appliances. Exploiting a Bottom-up approach based on Monte Carlo Non Homogeneous Semi-Markov, we provide household end-user behaviours and realistic households load profiles on a daily as well as on a weekly basis, for either weekdays and weekends. The proposed approach overcomes limitations of state-of-art solutions that do not consider neither the time-dependency of the probability of performing specific activities in a house, nor their duration, or are limited in the type of probability distributions they can model. On top of that, it provides outcomes that are not limited on a per-day basis. The range of available space and time resolutions span from single household to district and from second to year, respectively, featuring multi-level aggregation of the simulation outcomes. To demonstrate the accuracy of our model, we present experimental results obtained simulating realistic populations in a period covering a whole calendar year and analyse our model’s outcome at different scales. Then, we compare such results with three different data-sets that provide real load consumption at household, national and European levels, respectively

Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations

Computer-aided analysis of biological images typically requires extensive training on large-scale annotated datasets, which is not viable in many situations. In this paper, we present Generative Adversarial Network Discriminator Learner (GAN-DL), a novel self-supervised learning paradigm based on the StyleGAN2 architecture, which we employ for self-supervised image representation learning in the case of fluorescent biological images

Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations: a COVID-19 case-study

Computer-aided analysis of biological images typically requires extensive training on large-scale annotated datasets, which is not viable in many situations. In this paper we present GAN-DL, a Discriminator Learner based on the StyleGAN2 architecture, which we employ for self-supervised image representation learning in the case of fluorescent biological images. We show that Wasserstein Generative Adversarial Networks combined with linear Support Vector Machines enable high-throughput compound screening based on raw images. We demonstrate this by classifying active and inactive compounds tested for the inhibition of SARS-CoV-2 infection in VERO and HRCE cell lines. In contrast to previous methods, our deep learning based approach does not require any annotation besides the one that is normally collected during the sample preparation process. We test our technique on the RxRx19a Sars-CoV-2 image collection. The dataset consists of fluorescent images that were generated to assess the ability of regulatory-approved or in late-stage clinical trials compound to modulate the in vitro infection from SARS-CoV-2 in both VERO and HRCE cell lines. We show that our technique can be exploited not only for classification tasks, but also to effectively derive a dose response curve for the tested treatments, in a self-supervised manner. Lastly, we demonstrate its generalization capabilities by successfully addressing a zero-shot learning task, consisting in the categorization of four different cell types of the RxRx1 fluorescent images collection

Applying Textural Features to the Classification of HEp-2 Cell Patterns in IIF images

The analysis of anti-nuclear antibodies in HEp-2 cells by indirect immunofluorescence (IIF) is fundamental for the diagnosis of important immune pathologies; in particular, classifying the staining pattern of the cell is critical for the differential diagnosis of several types of diseases. Current tests based on human evaluation are time-consuming and suffer from very high variability, which impacts on the reliability of the results. As a solution to this problem, in this work we propose a technique that performs automated classification of the staining pattern. Our method combines textural feature extraction and a two-step feature selection scheme to select a limited number of image attributes that are best suited to the classification purpose and then recognizes the staining pattern by means of a Support Vector Machine module. Experiments on IIF images showed that our method is able to identify staining patterns with average accuracy of about 87%

Classification of HEp-2 staining patterns in ImmunoFluorescence images. Comparison of Support Vector Machines and Subclass Discriminant Analysis strategies

nti-nuclear antibodies test is based on the visual evaluation of the intensity and staining pattern in HEp-2 cell slides by means of indirect immunofluorescence (IIF) imaging, revealing the presence of autoantibodies responsible for important immune pathologies. In particular, the categorization of the staining pattern is crucial for differential diagnosis, because it provides information about autoantibodies type. Their manual classification is very time-consuming and not very reliable, since it depends on the subjectivity and on the experience of the specialist. This motivates the growing demand for computer-aided solutions able to perform staining pattern classification in a fully automated way. In this work we compare two classification techniques, based respectively on Support Vector Machines and Subclass Discriminant Analysis. A set of textural features characterizing the available samples are first extracted. Then, a feature selection scheme is applied in order to produce different datasets, containing a limited number of image attributes that are best suited to the classification purpose. Experiments on IIF images showed that our computer-aided method is able to identify staining patterns with an average accuracy of about 91% and demonstrate, in this specific problem, a better performance of Subclass Discriminant Analysis with respect to Support Vector Machine