Real-time 3D analysis during electron tomography using tomviz

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high quality tomogram is available within 30 minutes. Real time tomography is integrated into tomviz, an open source and cross platform 3D analysis tool that contains intuitive graphical user interfaces (GUI) to enable any scientist to characterize biological and material structure in 3D

HEXRD/hexrdgui: Release 1.0.0

<p>HEXRDGUI 1.0.0 includes major infrastructure upgrades, osx-arm64 packages, and a few new features and bug fixes. Below are a few highlights:</p> <ul> <li>Upgraded to Python3.11, resulting in noticeable performance improvements</li> <li>Upgraded to PySide6, which fixed some issues with the GUI interface</li> <li>Added conda packages for osx-arm64 (Apple computers after 2019)</li> <li>Added zoom box for raw view with summation plots</li> <li>Overhauled and simplified threshold masking</li> <li>Added ability to translate and rotate rectangle/ellipse masks</li> <li>Added configuration options, including changing font size and CPU limit</li> <li>Implemented numerous other minor improvements and bug fixes</li> </ul> <p>NOTE: you must create a new environment for this upgrade, so you should delete your old HEXRDGUI environment first. The install instructions have also changed. Please see here for updated instructions: https://hexrdgui.readthedocs.io/en/latest/installing/</p> <p>In particular, Python3.11 is now required, and installing/updating the prerelease is now simpler. For example, installing the prerelease is now as follows:</p> <pre><code class="language-bash">conda install -c hexrd/label/prerelease -c conda-forge python=3.11 hexrdgui </code></pre&gt

ImagingDataCommons/IDC-Tutorials: latest

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ImagingDataCommons/IDC-Tutorials: RSNA2023

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HEXRD/hexrd: Release 0.9.4

<ul> <li>Added support for Python3.11, resulting in noticeable performance improvements</li> <li>Added conda packages for osx-arm64 (Apple computers after 2019)</li> <li>Implemented build time optimization that results in performance improvements</li> <li>Added ability to cancel fit-grains programmatically</li> <li>Changed PXRDIP default polar angle to 67.5</li> <li>Improved TARDIS distance between plates constraint</li> <li>Implemented a few bug fixes, including one with memoization</li> </ul&gt

HEXRD/hexrdgui: Release 0.9.6

Many new features and improvements have been added in this release: many help buttons have been added throughout the program that link to pages in the documentation support for a cylindrical detector (used primarily in TARDIS currently) new Rygg pinhole distortion method (used primarily for TARDIS and PXRDIP) added stereographic view added Q scattering vector to mouse hover info as well as it being an option for the polar x-axis added azimuthal overlay plots in the polar view new structureless calibration workflow support for GEL files fit grains is now much faster, thanks to some transform function updates in HEXRD 0.9.3 fixed export of HEDM workflow many improvements to masking streamlined the LLNL import tool added reflections selection helper added option to perform relative scaling for structure factor added some command-line arguments added ability to export polar view to Mau

HEXRD/hexrd: Release 0.9.3

A variety of new features have been added, including: support for a cylindrical detector (used primarily in TARDIS currently) new Rygg pinhole distortion method (used primarily for TARDIS and PXRDIP) new structureless calibration class support for GEL files For the HEDM workflow: large performance improvements to fit-grains (including through the use of updated C transforms, and a major reduction in the amount of memory used) namedtuple grains output fixed an HKL reset issue in fit-grains new options for selecting which HKLs to exclude when running from the CL

Kitware/itk-vtk-viewer: v14.46.1

<h2><a href="https://github.com/kitware/itk-vtk-viewer/compare/v14.46.0...v14.46.1">14.46.1</a> (2023-12-19)</h2> <h3>Bug Fixes</h3> <ul> <li>default label image weight for background label is 0.0 (<a href="https://github.com/kitware/itk-vtk-viewer/commit/cd25476294c8cc751f7c440e486fa2b50118c0b9">cd25476</a>)</li> </ul&gt

Kitware/itk-vtk-viewer: v14.50.0

<h1><a href="https://github.com/kitware/itk-vtk-viewer/compare/v14.49.0...v14.50.0">14.50.0</a> (2024-01-09)</h1> <h3>Features</h3> <ul> <li><strong>ItkVtkViewProxy:</strong> move scale bar to upper left (<a href="https://github.com/kitware/itk-vtk-viewer/commit/d3051a5902209af357c20afdf7b1b3ffba537162">d3051a5</a>)</li> <li><strong>TranferFunctionEditor:</strong> upgrade for axis labels (<a href="https://github.com/kitware/itk-vtk-viewer/commit/190d81d4d19675b505d97d91f02b13522c41a771">190d81d</a>)</li> </ul&gt

Real-time 3D analysis during electron tomography using tomviz.

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D