Virtual airways heatmaps to optimize point of entry location in lung biopsy planning systems

Purpose: We present a virtual model to optimize point of entry (POE) in lung biopsy planning systems. Our model allows to compute the quality of a biopsy sample taken from potential POE, taking into account the margin of error that arises from discrepancies between the orientation in the planning simulation and the actual orientation during the operation. Additionally, the study examines the impact of the characteristics of the lesion. Methods: The quality of the biopsy is given by a heatmap projected onto the skeleton of a patient-specific model of airways. The skeleton provides a 3D representation of airways structure, while the heatmap intensity represents the potential amount of tissue that it could be extracted from each POE. This amount of tissue is determined by the intersection of the lesion with a cone that represents the uncertainty area in the introduction of biopsy instruments. The cone, lesion, and skeleton are modelled as graphical objects that define a 3D scene of the intervention. Results: We have simulated different settings of the intervention scene from a single anatomy extracted from a CT scan and two lesions with regular and irregular shapes. The different scenarios are simulated by systematic rotation of each lesion placed at different distances from airways. Analysis of the heatmaps for the different settings show a strong impact of lesion orientation for irregular shape and the distance for both shapes. Conclusion: The proposed heatmaps help to visually assess the optimal POE and identify whether multiple optimal POEs exist in different zones of the bronchi. They also allow us to model the maximum allowable error in navigation systems and study which variables have the greatest influence on the success of the operation. Additionally, they help determine at what point this influence could potentially jeopardize the operation.

Diagnosising Helicobacter pylori using AutoEncoders and Limited Annotations through Anomalous Staining Patterns in IHC Whole Slide Images

Purpose: This work addresses the detection of Helicobacter pylori (H. pylori) in histological images with immunohistochemical staining. This analysis is a time demanding task, currently done by an expert pathologist that visually inspects the samples. Given the effort required to localise the pathogen in images, a limited number of annotations might be available in an initial setting. Our goal is to design an approach that, using a limited set of annotations, is capable of obtaining results good enough to be used as a support tool. Methods: We propose to use autoencoders to learn the latent patterns of healthy patches and formulate a specific measure of the reconstruction error of the image in HSV space. ROC analysis is used to set the optimal threshold of this measure and the percentage of positive patches in a sample that determines the presence of H. pylori. Results: Our method has been tested on an own database of 245 Whole Slide Images (WSI) having 117 cases without H. pylori and different density of the bacteria in the remaining ones. The database has 1211 annotated patches, with only 163 positive patches. This dataset of positive annotations was used to train a baseline thresholding and an SVM using the features of a pre-trained RedNet18 and ViT models. A 10-fold cross-validation shows that our method has better performance with 91% accuracy, 86% sensitivity, 96% specificity and 0.97 AUC in the diagnosis of H. pylori. Conclusion: Unlike classification approaches, our shallow autoencoder with threshold adaptation for the detection of anomalous staining is able to achieve competitive results with a limited set of annotated data. This initial approach is good enough to be used as a guide for fast annotation of infected patches.

Diagnosis of Helicobacter pylori using AutoEncoders for the Detection of Anomalous Staining Patterns in Immunohistochemistry Images

This work addresses the detection of Helicobacter pylori a bacterium classified since 1994 as class 1 carcinogen to humans. By its highest specificity and sensitivity, the preferred diagnosis technique is the analysis of histological images with immunohistochemical staining, a process in which certain stained antibodies bind to antigens of the biological element of interest. This analysis is a time demanding task, which is currently done by an expert pathologist that visually inspects the digitized samples. We propose to use autoencoders to learn latent patterns of healthy tissue and detect H. pylori as an anomaly in image staining. Unlike existing classification approaches, an autoencoder is able to learn patterns in an unsupervised manner (without the need of image annotations) with high performance. In particular, our model has an overall 91% of accuracy with 86\% sensitivity, 96% specificity and 0.97 AUC in the detection of H. pylori.