This new alternate approach to data processing for analyses that traditionally employed grid-based counting methods is necessary because it removes a user-imposed coordinate system that not only limits an analysis but also may introduce errors. We have modified the widely used "binomial" analysis for APT data by replacing grid-based counting with coordinate-independent nearest neighbour identification, improving the measurements and the statistics obtained, allowing quantitative analysis of smaller datasets, and datasets from non-dilute solid solutions. It also allows better visualisation of compositional fluctuations in the data. Our modifications include:.•using spherical k-atom blocks identified by each detected atom's first k nearest neighbours.•3D data visualisation of block composition and nearest neighbour anisotropy.•using z-statistics to directly compare experimental and expected composition curves. Similar modifications may be made to other grid-based counting analyses (contingency table, Langer-Bar-on-Miller, sinusoidal model) and could be instrumental in developing novel data visualisation options.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472836 | PMC |
http://dx.doi.org/10.1016/j.mex.2014.02.001 | DOI Listing |
Proc SPIE Int Soc Opt Eng
February 2024
Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, CO.
Energy sensitive and photon counting detectors can provide improved tissue visualization and material quantification capabilities in Cone Beam Computed Tomography (CBCT) systems. However, their implementation in CBCT systems is more challenging, which is in part due to high fluence of scattered X-rays in wide cone angle CBCT geometry. Specifically, high scatter contamination in lower energy spectrum challenges reconstruction of high fidelity CBCT images by using lower energy X-rays.
View Article and Find Full Text PDFJ Surg Res
March 2024
Faculty of Medicine, Institute of Clinical Medicine, Vilnius University, Vilnius, Lithuania.
Introduction: Our previous research demonstrated that CD8+ cell density profiling using a hexagonal grid-based digital image analysis method provides predictors of patient outcomes after liver resection due to hepatocellular carcinoma (HCC). Continuing our study, we have further investigated the applicability of the methodology to patients receiving a liver transplant for HCC.
Methods: The retrospective study enrolled patients with HCC who underwent liver transplantation (LT) at the Vilnius University Hospital Santaros Clinics between 2007 and 2020.
Arch Pathol Lab Med
January 2024
From the Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden.
Context.—: The immune microenvironment is involved in fundamental aspects of tumorigenesis, and immune scores are now being developed for clinical diagnostics.
Objective.
Cancers (Basel)
January 2023
Faculty of Medicine, Institute of Biomedical Sciences, Department of Pathology, Forensic Medicine and Pharmacology, Vilnius University, 03101 Vilnius, Lithuania.
J Chem Inf Model
October 2021
YASARA Biosciences GmbH, Wagramer Str. 25/3/45, 1220 Vienna, Austria.
Building and displaying all-atom models of biomolecular structures with millions or billions of atoms, like virus particles or cells, remain a challenge due to the sheer size of the data, the required levels of automated building, and the visualization limits of today's graphics hardware. Based on concepts introduced with the CellPack program, we report new algorithms to create such large-scale models using an intermediate coarse-grained "pet representation" of biomolecules with 1/10th the normal size. Pet atoms are placed such that they optimally trace the surface of the original molecule with just ∼1/50th the original atom number and are joined with covalent bonds.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!