Inferring a Third Spatial Dimension from 2D Histological Images

Histological images are obtained by transmitting light through a tissue specimen that has been stained in order to produce contrast. This process results in 2D images of the specimen that has a three-dimensional structure. In this paper, we propose a method to infer how the stains are distributed in the direction perpendicular to the surface of the slide for a given 2D image in order to obtain a 3D representation of the tissue. This inference is achieved by decomposition of the staining concentration maps under constraints that ensure realistic decomposition and reconstruction of the original 2D images. Our study shows that it is possible to generate realistic 3D images making this method a potential tool for data augmentation when training deep learning models.Comment: IEEE International Symposium on Biomedical Imaging (ISBI), 201

Inductive Visual Localisation: Factorised Training for Superior Generalisation

End-to-end trained Recurrent Neural Networks (RNNs) have been successfully applied to numerous problems that require processing sequences, such as image captioning, machine translation, and text recognition. However, RNNs often struggle to generalise to sequences longer than the ones encountered during training. In this work, we propose to optimise neural networks explicitly for induction. The idea is to first decompose the problem in a sequence of inductive steps and then to explicitly train the RNN to reproduce such steps. Generalisation is achieved as the RNN is not allowed to learn an arbitrary internal state; instead, it is tasked with mimicking the evolution of a valid state. In particular, the state is restricted to a spatial memory map that tracks parts of the input image which have been accounted for in previous steps. The RNN is trained for single inductive steps, where it produces updates to the memory in addition to the desired output. We evaluate our method on two different visual recognition problems involving visual sequences: (1) text spotting, i.e. joint localisation and reading of text in images containing multiple lines (or a block) of text, and (2) sequential counting of objects in aerial images. We show that inductive training of recurrent models enhances their generalisation ability on challenging image datasets.Comment: In BMVC 2018 (spotlight

Non-rigid registration on histopathological breast cancer images using deep learning

Cancer is one of the leading causes of death in the world, in particular, breast cancer is the most frequent in women. Early detection of this disease can significantly increase the survival rate. However, the diagnosis is difficult and time-consuming. Hence, many artificial intelligence applications have been deployed to speed up this procedure. In this MSc thesis, we propose an automatic framework that could help pathologists to improve and speed up the first step of the diagnosis of cancer. It will facilitate the cross-slide analysis of different tissue samples extracted from a selected area where cancer could be present. It will allow either pathologists to easily compare tissue structures to understand the disease's seriousness or the automatic analysis algorithms to work with several stains at once. The proposed method tries to align pairs of high-resolution histological images, curving and stretching part of the tissue by applying a deformation field to one image of the pair

Multimodal perception of histological images for persons blind or visually impaired

Currently there is no suitable substitute technology to enable blind or visually impaired (BVI) people to interpret visual scientific data commonly generated during lab experimentation in real time, such as performing light microscopy, spectrometry, and observing chemical reactions. This reliance upon visual interpretation of scientific data certainly impedes students and scientists that are BVI from advancing in careers in medicine, biology, chemistry, and other scientific fields. To address this challenge, a real-time multimodal image perception system is developed to transform standard laboratory blood smear images for persons with BVI to perceive, employing a combination of auditory, haptic, and vibrotactile feedbacks. These sensory feedbacks are used to convey visual information through alternative perceptual channels, thus creating a palette of multimodal, sensorial information. A Bayesian network is developed to characterize images through two groups of features of interest: primary and peripheral features. Causal relation links were established between these two groups of features. Then, a method was conceived for optimal matching between primary features and sensory modalities. Experimental results confirmed this real-time approach of higher accuracy in recognizing and analyzing objects within images compared to tactile images

Review of data types and model dimensionality for cardiac DTI SMS-related artefact removal

As diffusion tensor imaging (DTI) gains popularity in cardiac imaging due to its unique ability to non-invasively assess the cardiac microstructure, deep learning-based Artificial Intelligence is becoming a crucial tool in mitigating some of its drawbacks, such as the long scan times. As it often happens in fast-paced research environments, a lot of emphasis has been put on showing the capability of deep learning while often not enough time has been spent investigating what input and architectural properties would benefit cardiac DTI acceleration the most. In this work, we compare the effect of several input types (magnitude images vs complex images), multiple dimensionalities (2D vs 3D operations), and multiple input types (single slice vs multi-slice) on the performance of a model trained to remove artefacts caused by a simultaneous multi-slice (SMS) acquisition. Despite our initial intuition, our experiments show that, for a fixed number of parameters, simpler 2D real-valued models outperform their more advanced 3D or complex counterparts. The best performance is although obtained by a real-valued model trained using both the magnitude and phase components of the acquired data. We believe this behaviour to be due to real-valued models making better use of the lower number of parameters, and to 3D models not being able to exploit the spatial information because of the low SMS acceleration factor used in our experiments.Comment: 11 pages, 3 tables, 1 figure. To be published at the STACOM workshop, MICCAI 202

Inferring the location of neurons within an artificial network from their activity

Inferring the connectivity of biological neural networks from neural activation data is an open problem. We propose that the analogous problem in artificial neural networks is more amenable to study and may illuminate the biological case. Here, we study the specific problem of assigning artificial neurons to locations in a network of known architecture, specifically the LeNet image classifier. We evaluate a supervised learning approach based on features derived from the eigenvectors of the activation correlation matrix. Experiments highlighted that for an image dataset to be effective for accurate localisation, it should fully activate the network and contain minimal confounding correlations. No single image dataset was found that resulted in perfect assignment, however perfect assignment was achieved using a concatenation of features from multiple image datasets