Visualization

MotionCor2

MotionCor2 uses multi-GPU acceleration to correct anisotropic cryo-electron microscopy images at the single pixel level across the whole frame, making it suitable for single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

VisIt

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool for visualizing data defined on two- and three-dimensional structured and unstructured meshes.

 

Texlive

TeX Live is a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro pacakges, and fonts that are free software, including support for many languages around the world.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

Scipion

SCIPION is an image processing framework fo robtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

Availability and Restrictions

Versions

The following versions are available on OSC clusters:

xcpEngine

The XCP imaging pipeline (XCP system) is a free, open-source software package for processing of multimodal neuroimages. The XCP system uses a modular design to deploy analytic routines from leading MRI analysis platforms, including FSL, AFNI, and ANTs.

Availability and Restrictions

Versions

xcpEngine is available on Pitzer cluster. These are the versions currently available:

Software Refresh - May 2020

OSC will be refreshing the software stack for Owens and Pitzer on May 19, 2020. This will be done in a system-wide downtime. During the software refresh, some default versions will be changed to be more up-to-date. Information about the new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.

Connectome Workbench

Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.

Availability and Restrictions

Versions

Connectome Workbench is available on Owens and Pitzer clusters. These are the versions currently available:

Transmission3d

Transmission3d is a 3-dimensional, multi-body gear contact analysis software capable of modeling complex gear systems developed by Ansol (Advanced Numeric Solutions). Multiple gear types, including: Helical, Straight Bevel, Spiral Bevel, Hypoids, Beveloids and Worms can be modeled. Multiple bearing types, as well as complex shafts, carriers and housings can also be modeled with the software. A variety of output data options including tooth bending stress, contact patterns, and displacement are also available.

ffmpeg

FFmpeg is a free software project, the product of which is a vast software suite of libraries and programs for handling video, audio, and other multimedia files and streams.

Availability and Restrictions

Versions

The following versions of FFmpeg are available on OSC clusters:

Blender

Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.

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