Open Source Linux Data Visualization Software - Page 8
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Data Visualization Software for Linux
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PyMOL Molecular Graphics System
PyMOL is an OpenGL based molecular visualization system
The Open-Source PyMOL repository has been moved to github: https://github.com/schrodinger/pymol-open-source We still use the pymol-users mailing list here on sourceforge. Please subscribe for community support: https://pymol.org/maillist (Note: SourceForge email newsletter and special offers are optional and can be unchecked) The PyMOL community wiki has its own home: https://pymolwiki.org/ -
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SPX
A simple & straight-to-the-point PHP profiling extension
SPX, which stands for Simple Profiling eXtension, is just another profiling extension for PHP. It differentiates itself from other similar extensions as being totally free and confined to your infrastructure (i.e. no data leaks to a SaaS). Very simple to use: just set an environment variable (command line) or switch on a radio button (web request) to profile your script. Thus, you are free of manually instrumenting your code (Ctrl-C a long running command line script is even supported). Using a dedicated browser extension or command line launcher. Multi metrics capable: 22 are currently supported (various time & memory metrics, included files, objects in use, I/O...). Able to collect data without losing context. For example Xhprof (and potentially its forks) aggregates data per caller / callee pairs, which implies the loss of the full call stack and forbids timeline or Flamegraph based analysis. -
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TIGRE
TIGRE: Tomographic Iterative GPU-based Reconstruction Toolbox
TIGRE is an open-source toolbox for fast and accurate 3D tomographic reconstruction for any geometry. Its focus is on iterative algorithms for improved image quality that have all been optimized to run on GPUs (including multi-GPUs) for improved speed. It combines the higher-level abstraction of MATLAB or Python with the performance of CUDA at a lower level in order to make it both fast and easy to use. TIGRE is free to download and distribute: use it, modify it, add to it, and share it. Our aim is to provide a wide range of easy-to-use algorithms for the tomographic community "off the shelf". We would like to build a stronger bridge between algorithm developers and imaging researchers/clinicians by encouraging and supporting contributions from both sides to TIGRE. -
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TransPose
PyTorch Implementation for "TransPose, Keypoint localization
TransPose is a human pose estimation model based on a CNN feature extractor, a Transformer Encoder, and a prediction head. Given an image, the attention layers built in Transformer can efficiently capture long-range spatial relationships between keypoints and explain what dependencies the predicted keypoints locations highly rely on. -
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XLSX.jl
Excel file reader and writer for the Julia language
XLSX.jl is a Julia package to read and write Excel spreadsheet files. Internally, an Excel XLSX file is just a Zip file with a set of XML files inside. The formats for these XML files are described in the Standard ECMA-376. This package follows the EMCA-376 to parse and generate XLSX files. -
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XPEViewer
PE file viewer/editor for Windows, Linux and MacOS
XPEViewer is a cross-platform viewer and editor for Microsoft Portable Executable files used by Windows applications. It is designed for developers, malware analysts, and reverse engineers who need to inspect executable structures in detail. The application combines PE parsing with tools for examining binary data, disassembly, symbols, regions, entropy, and memory layout. Integrated hexadecimal viewing and editing provide direct access to raw file contents. The project also incorporates signature scanning, extraction, unpacking, and related analysis components from the developer's wider tool ecosystem. Builds are available for Windows, Linux, and macOS despite the analyzed format being primarily associated with Windows. Its modular Qt-based codebase supports both continued development and specialized binary-analysis workflows. -
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BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
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SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.
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Kabeja is a java library for parsing DXF and converting to SVG (dxf2svg). The library supports the SAX-api and can integrated into other applications (Cocoon,Batik). Tools for converting svg to jpeg, tiff, png and pdf are included .
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samscope
A lightweight OpenGL SAM/BAM viewer
A lightweight OpenGL based interactive SAM/BAM viewer. Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments. -
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High Dynamic Range Visual Difference Predictor (HDR VDP) is a perceptual metric that can predict whether differences between two images are visible to the human observer or not.
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FractalNow
Fast, advanced, multi-platform fractal generator
FractalNow provides users with tools to generate pictures of various types of fractals quickly and easily. It is made of both a command line tool, FractalNow, and a graphical tool, QFractalNow. The graphical tool, based on Qt library, allows users to explore fractals intuitively and generate pictures. Both tools are entirely multi-threaded and implement advanced algorithms and heuristics that make computation very fast compared to most existing free fractal generators. -
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JaxoDraw
JaxoDraw: Feynman Diagrams made easy!
JaxoDraw is a tool to generate Feynman diagrams in a mouse click-and-drag fashion. Graphs can be exported to a variety of graphics formats and arbitrary latex code can be used for labels to produce high-quality publishing-style figures. -
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UPDATE: Chromium is no longer updated or maintained. The project is frozen. Chromium is a flexible framework for scalable real-time rendering on clusters of workstations, derived from the Stanford WireGL project code base.
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The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging (http://www.svi.nl/) for parallel batch deconvolutions.
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QUAST
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. It is maintained by the Gurevich lab at HIPS (https://helmholtz-hips.de/en/hmsb). For the most up-to-date description, please visit http://quast.sf.net. Below are just some highlights. QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). A comprehensive analysis results in summary tables (in plain text, tab-separated, and LaTeX formats) and colorful plots. The tool also produces web-based reports condensing all information in one easy-to-navigate file. QUAST and its three follow-up papers (MetaQUAST, Icarus, QUAST-LG) papers were published in Bioinformatics; the last paper (WebQUAST) is out in Nucl Acid Research. -
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SMILI
Scientific Visualisation Made Easy
The Simple Medical Imaging Library Interface (SMILI), pronounced 'smilie', is an open-source, light-weight and easy-to-use medical imaging viewer and library for all major operating systems. The main sMILX application features for viewing n-D images, vector images, DICOMs, anonymizing, shape analysis and models/surfaces with easy drag and drop functions. It also features a number of standard processing algorithms for smoothing, thresholding, masking etc. images and models, both with graphical user interfaces and/or via the command-line. See our YouTube channel for tutorial videos via the homepage. The applications are all built out of a uniform user-interface framework that provides a very high level (Qt) interface to powerful image processing and scientific visualisation algorithms from the Insight Toolkit (ITK) and Visualisation Toolkit (VTK). The framework allows one to build stand-alone medical imaging applications quickly and easily. -
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atomes
Analysis, visualization, edition of 3D atomistic models
atomes is a Free (Open Source) cross-platform software licensed under the terms of the Affero GPL v3+ license. atomes is a toolbox developed to analyze, to visualize and to create/edit 3D atomic scale models. atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: - Classical MD : DL-POLY and LAMMPS - ab-initio MD : CPMD and CP2K - QM-MM MD : CPMD and CP2K atomes is developed by Dr. Sébastien Le Roux, research engineer for the CNRS Dr. Sébastien Le Roux works at the Institut de Physique et Chimie des Matériaux de Strasbourg. -
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CThruView is an image viewer that allows mouse clicks to go through the image. Use it as tracing paper or splash screen. The image can be made semi-transparent, flipped, rotated, zoomed, always on top, clipped, moved, hidden and centered.
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PixelLight
PixelLight is a cross-platform application framework
PixelLight is a cross-platform application framework for any kind of 3D applications like games, interactive simulations or visualizations. It's written in C++ and has been designed with flexibility and extensibility as one of it's main goals. -
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GPlates
Interactive visualization of plate tectonics.
GPlates is a plate-tectonics program. Manipulate reconstructions of geological and paleo-geographic features through geological time. Interactively visualize vector, raster and volume data. PyGPlates is the GPlates Python library. Get fine-grained access to GPlates functionality in your Python scripts. -
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ACME.jl
Analog Circuit Modeling and Emulation for Julia
ACME is a Julia package for the simulation of electrical circuits, focusing on audio effect circuits. It allows one to programmatically describe a circuit in terms of elements and connections between them and then automatically derive a model for the circuit. The model can then be run on varying input data. -
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ArgParse.jl
Package for parsing command-line arguments to Julia programs
ArgParse.jl is a package for parsing command-line arguments to Julia programs. -
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Bayesian Statistics
This repository holds slides and code for a full Bayesian statistics
This repository holds slides and code for a full Bayesian statistics graduate course. Bayesian statistics is an approach to inferential statistics based on Bayes' theorem, where available knowledge about parameters in a statistical model is updated with the information in observed data. The background knowledge is expressed as a prior distribution and combined with observational data in the form of a likelihood function to determine the posterior distribution. The posterior can also be used for making predictions about future events. Bayesian statistics is a departure from classical inferential statistics that prohibits probability statements about parameters and is based on asymptotically sampling infinite samples from a theoretical population and finding parameter values that maximize the likelihood function. Mostly notorious is null-hypothesis significance testing (NHST) based on p-values. -
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CNN Explainer
Learning Convolutional Neural Networks with Interactive Visualization
In machine learning, a classifier assigns a class label to a data point. For example, an image classifier produces a class label (e.g, bird, plane) for what objects exist within an image. A convolutional neural network, or CNN for short, is a type of classifier, which excels at solving this problem! A CNN is a neural network: an algorithm used to recognize patterns in data. Neural Networks in general are composed of a collection of neurons that are organized in layers, each with their own learnable weights and biases. Let’s break down a CNN into its basic building blocks. A tensor can be thought of as an n-dimensional matrix. In the CNN above, tensors will be 3-dimensional with the exception of the output layer. A neuron can be thought of as a function that takes in multiple inputs and yields a single output. The outputs of neurons are represented above as the red → blue activation maps.
