Machine Learning for Gastric Cancer Detection

The objective of this study is the investigation of the potential value of a logistic regression model for the classification of gastric cytological data. The model was based on the morphological features of cell nuclei. The aim was the discrimination of benign from malignant nuclei and subsequently patients. Cytological images of gastric smears were analyzed by an image analysis system capable to extract cell nuclear features. Measurements from 50% of the patients were selected as a training set for model creation, while the measurements from the remaining patients were used as test set to validate the results. Furthermore, a model for the classification of individual patients, based on the classification of their cell nuclei has been developed. This approach set gave a correct classification at the level of 90% on the training and test sets on the nuclear level. Concluding the application of morphometric feature selection in combination with logistic regression may offer useful and complementary information about the potential of malignancy of gastric nuclei and patient cases.

Computing Bone Morphometric Feature Maps from 3-Dimensional Images

This document describes a new remote module implemented for the Insight Toolkit (ITK), itkBoneMorphometry. This module contains bone analysis filters that compute features from N-dimensional images that represent the internal architecture of bone. The computation of the bone morphometry features in this module is based on well known methods. The two filters contained in this module are itkBoneMorphometryFeaturesFilter. which computes a set of features that describe the whole input image in the form of a feature vector, and itkBoneMorphometryFeaturesImageFilter, which computes an N-D feature map that locally describes the input image (i.e. for every voxel). itkBoneMorphometryFeaturesImageFilter can be configured based in the locality of the desired morphometry features by specifying the neighborhood size. This paper is accompanied by the source code, the input data, the choice of parameters and the output data that we have used for validating the algorithms described. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.

A population MRI brain template and analysis tools for the macaque

The use of standard anatomical templates is common in human neuroimaging, as it facilitates data analysis and comparison across subjects and studies. For non-human primates, previous in vivo templates have lacked sufficient contrast to reliably validate known anatomical brain regions and have not provided tools for automated single-subject processing. Here we present the “National Institute of Mental Health Macaque Template”, or NMT for short. The NMT is a high-resolution in vivo MRI template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, we generated maps of tissue segmentation and cortical thickness. Surface reconstructions and transformations to previously published digital brain atlases are also provided. We further provide an analysis pipeline using the NMT that automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies.

Manifestations and causes of meromixis in lakes resulting from mineral extraction in Czechia

Anthropogenic lakes (lakes that have developed in mined-out pits as a consequence of mineral raw material mining) exhibit many interesting phenomena. Specific water features are the most remarkable, including physical, chemical and the biological characteristics. Other very specific morphometric feature of anthropogenic lake basins include the unusual location of the lake’s water surface: often several dozen meters below the adjacent terrain and the specific character of the mined-out raw materials. All of these factors affect the qualitative characteristics of lake’s water, even decades after flooding. The interaction of the factors mentioned above has resulted in the creation of a permanent meromixis in some anthropogenic lakes. The author’s primary objectives are to present some physical and chemical symptoms of meromixis at selected localities, to discuss the mutual interaction between the physical and chemical characteristics of lake water and to explore some probable causes of the origin of meromixis at the selected localities.