Automatic layers recognition of the wall of the stomach and colon on whole slide images is an extremely urgent task in digital pathology as it can be used for automatic determining the depth of invasion of the digestive tract tumors. In this paper we propose a new CNN-based method of automatic tissue type recognition on whole slide histological images. We also describe an effective pipeline of training that uses 2 different training datasets. The proposed method of automatic tissue type recognition achieved 0.929 accuracy and 0.903 balanced accuracy on CRC-VAL-HE-7K dataset for 9-types classification and 0.98 accuracy and 0.926 balanced accuracy on the test subset of whole slide images from PATH-DT- MSU dataset for 5-types classification. The developed method makes it possible to classify the areas corresponding to the gastric own mucous glands in the lamina propria and also to distinguish the tubular structures of a highly differentiated gastric adenocarcinoma with normal glands.

Mucous glands is an important diagnostic element in digestive pathology. The first step of differential diagnosis of colon polyps in order to assess their malignant potential is gland segmentation. The process of mucous glands segmentation is challenging as the glands not only needed to be separated from a background but also individually identified to obtain reliable morphometric criteria for quantitative diagnostic methods. We propose a new convolutional neural network for mucous gland segmentation that takes into account glands’ contours and can be used for gland instance segmentation. Training and evaluation of the network was performed on a standard Warwick-QU dataset as well as on the collected PATH-DT-MSU dataset of histological images obtained from hematoxylin and eosin staining of paraffin sections of colon biopsy material collected by our Pathology department. The collected PATH-DT-MSU dataset will be available at http://imaging.cs.msu.ru/en/research/histology.

The use of modern approaches based on convolutional neural networks (CNNs) for segmentation of whole slide images (WSIs) helps pathologists obtain more stable and quantitative analysis results and improve diagnosis objectivity. But working with WSIs is extremely difficult due to their resolution and size. To solve this problem in this paper we for the first time present PathScribe – a new universal cross-platform cloud-based tool for comfortable viewing and manipulating large collections of WSIs on almost any device, including tablets and smartphones. We also consider the important problem of automatic tissue type recognition on WSIs and present the WSS1 and WSS2 subsets of PATH-DT-MSU dataset representing a collection of high-quality WSIs of digestive tract tumors with tissue type area annotations. We also propose a new CNN-based method of automatic tissue type recognition on WSIs. It achieved 0.929 accuracy on CRC-VAL-HE-7K dataset (9 classes) and 0.97 accuracy on PATH-DT-MSU-WSS1, WSS2 datasets (5 classes). The developed method allows classifying the areas corresponding to the gastric own mucous glands in the lamina propria and distinguishing the tubular structures of a highly differentiated gastric adenocarcinoma with normal glands.

Suppression of ringing artifacts in images is a well-known image restoration problem. Gibbs-ringing artifacts occur when, in the process of magnetic resonance imaging, the source data from the frequency domain are mapped onto the spatial domain by using the discrete Fourier transform. The artifacts are caused by the incompleteness of these data, which, in turn, is due to cutting off the high frequencies of the Fourier spectrum. In this paper, we propose a hybrid method for Gibbs-ringing artifact suppression in magnetic resonance images that combines a deep learning model and a classical non-machine-learning algorithm for Gibbs-ringing artifact suppression based on optimal subvoxel shifts.