Related papers: PDBImages: A Command Line Tool for Automated Macro…
The task of dimensionality reduction and visualization of high-dimensional datasets remains a challenging problem since long. Modern high-throughput technologies produce newer high-dimensional datasets having multiple views with relatively…
Motivation: The visualization and analysis of high-dimensional data are essential in biomedical research. There is a need for secure, scalable, and reproducible tools to facilitate data exploration and interpretation. Results: We introduce…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
Transport-Based Morphometry (TBM) has emerged as a new framework for 3D medical image analysis. By embedding images into a transport domain via invertible transformations, TBM facilitates effective classification, regression, and other…
PathDB is a Java-based graph database designed for in-memory data loading and querying. By utilizing Regular Path Queries (RPQ) and a closed path algebra, PathDB processes paths through its three main components: the parser, the logical…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Tracking single molecules is instrumental for quantifying the transport of molecules and nanoparticles in biological samples, e.g., in brain drug delivery studies. Existing intensity-based localisation methods are not developed for imaging…
JBotSim is a java library that offers basic primitives for prototyping, running, and visualizing distributed algorithms in dynamic networks. With JBotSim, one can implement an idea in minutes and interact with it ({\it e.g. }, add, move, or…
The need for fast diagnostic image viewing in zero footprint web applications and the ever increasing image sizes for new modalities such as digital pathology have painfully brought to light that the currently available image compression…
Modern bioimage analysis approaches are data hungry, making it necessary for researchers to scavenge data beyond those collected within their (bio)imaging facilities. In addition to scale, bioimaging datasets must be accompanied with…
We present a pipeline for unbiased and robust multimodal registration of neuroimaging modalities with minimal pre-processing. While typical multimodal studies need to use multiple independent processing pipelines, with diverse options and…
In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular…
In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…
Molecular visualization software has long supported research and education in chemical and structural sciences, but consumer devices constrained to 2D inputs and outputs pose two major challenges: they poorly convey 3D nature, and 3D…
The rapid development of tools for acquisition and storage of information has lead to the formation of enormous medical databases. The large quantity of data definitely surpasses the abilities of humans for efficient usage without…
Currently, a substantial volume of document data exists in an unstructured format, encompassing Portable Document Format (PDF) files and images. Extracting information from these documents presents formidable challenges due to diverse table…
Alterations in nuclear morphology are useful adjuncts and even diagnostic tools used by pathologists in the diagnosis and grading of many tumors, particularly malignant tumors. Large datasets such as TCGA and the Human Protein Atlas, in…
In mass spectrometry-based proteomics, experts usually project data onto a single set of reference sequences, overlooking the influence of common haplotypes (combinations of genetic variants inherited together from a parent). We recently…
The identification of metabolites from complex biological samples often involves matching experimental mass spectrometry data to signatures of compounds derived from massive chemical databases. However, misidentifications may result due to…
Scientific papers use schematic diagrams to communicate methods, workflows, and system structure, yet existing scientific-figure corpora often mix them with plots, screenshots, and photographs and rarely preserve document context. We…