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Xtra Library for Thermo Scientific Amira, Avizo and PerGeos Software
<!DOCTYPE html> <html lang="en" class="xtras xtras index" prefix="og:http://ogp.me/ns#"> <head> <title>Xtra Library for Thermo Scientific Amira, Avizo and PerGeos Software</title> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta name="description" content="Xtras"> <link rel="shortcut icon" href="/img/favicon.ico"> <link rel="canonical" href="https://www.thermofisher.com/software-em-3d-vis/xtra-library/how-to"/> <link type="text/css" rel="stylesheet" media="all" href="/software-em-3d-vis/xtra-library/vendors/owl.carousel.min.css?ver=^2.3.4"> <link type="text/css" rel="stylesheet" media="all" href="/software-em-3d-vis/xtra-library/vendors/owl.theme.default.min.css?ver=^2.3.4"> <link type="text/css" rel="stylesheet" media="all" href="/software-em-3d-vis/xtra-library/vendors/lightgallery.min.css"> <link type="text/css" rel="stylesheet" media="all" 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d-sm-block"> <div class="input-group"> <input name="search" type="text" class="form-control" placeholder="Search" aria-label="Search" value="" data-filters=""> <div class="input-group-append"> <button class="btn btn-primary btn-search" type="submit"><i class="fa fa-search"></i></button> </div> </div> </form> </div> </div> </nav> <section> <div class="container"> <div class="row"> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/amira-avizo-software-revamped-documentation" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2024/07/documentation_title-md.png" alt="Amira-Avizo Software Revamped Documentation"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/amira-avizo-software-revamped-documentation" title="Amira-Avizo Software Revamped Documentation">Amira-Avizo Software Revamped Documentation</a> </p> <p class="card-type"> <em><small>Demo</small></em> </p> <p class="card-text text-justify"> <small>1 Aug 2024</small> - This short video provides an overview of the changes we have made to improve the accessibility of the documentation for the Amira and Avizo Software. <a href="/software-em-3d-vis/xtra-library/xtras/amira-avizo-software-revamped-documentation">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/amira-avizo-software-revamped-documentation">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/segmentation-workroom-tutorial" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2024/05/UI screencapture-md.png" alt="Segmentation+ Workroom Tutorial"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/segmentation-workroom-tutorial" title="Segmentation+ Workroom Tutorial">Segmentation+ Workroom Tutorial</a> </p> <p class="card-type"> <em><small>Demo</small></em> </p> <p class="card-text text-justify"> <small>2 May 2024</small> - Discover the Segmentation+ workroom, a powerful tool for interactive 3D image segmentation. This tutorial offers a comprehensive overview of the segmentation process, covering essential principles and tools. <a href="/software-em-3d-vis/xtra-library/xtras/segmentation-workroom-tutorial">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/segmentation-workroom-tutorial">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-arithmetic-module" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2023/12/Arith-md.jpg" alt="How to Use the Arithmetic Module"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-arithmetic-module" title="How to Use the Arithmetic Module">How to Use the Arithmetic Module</a> </p> <p class="card-type"> <em><small>Demo</small></em> </p> <p class="card-text text-justify"> <small>2 Jan 2024</small> - This series of video tutorials introduces the Arithmetic module and examples of use cases. <a href="/software-em-3d-vis/xtra-library/xtras/how-to-arithmetic-module">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/how-to-arithmetic-module">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/trabecular-segmentation-workflow-for-murine-tibial-bone" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2023/11/snapshot-md.png" alt="Trabecular Segmentation Workflow for Murine Tibial Bone"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/trabecular-segmentation-workflow-for-murine-tibial-bone" title="Trabecular Segmentation Workflow for Murine Tibial Bone">Trabecular Segmentation Workflow for Murine Tibial Bone</a> </p> <p class="card-type"> <em><small>Recipe (hxrecipe), Project (hx, pgo), Demo, Data</small></em> </p> <p class="card-text text-justify"> <small>11 Dec 2023</small> - Here we provide a workflow to easily obtain the segmentation of trabecular bones. <a href="/software-em-3d-vis/xtra-library/xtras/trabecular-segmentation-workflow-for-murine-tibial-bone">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/trabecular-segmentation-workflow-for-murine-tibial-bone">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/visualize-identified-molecules-of-a-cryo-tomogram" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2023/11/VisualizeIdentifiedMoleculesOfACryotomogram-md.png" alt="Visualize Identified Molecules of a Cryo-Tomogram"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/visualize-identified-molecules-of-a-cryo-tomogram" title="Visualize Identified Molecules of a Cryo-Tomogram">Visualize Identified Molecules of a Cryo-Tomogram</a> </p> <p class="card-type"> <em><small>Python (pyscro), Project (hx, pgo)</small></em> </p> <p class="card-text text-justify"> <small>4 Dec 2023</small> - This Xtra provides the means to import results from template matching and visualize them with the Molecule Cloud View module. In addition, a module is provided to crop point clouds according to an ROI-box. <a href="/software-em-3d-vis/xtra-library/xtras/visualize-identified-molecules-of-a-cryo-tomogram">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/visualize-identified-molecules-of-a-cryo-tomogram">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/ai-assisted-tool-for-cryoem-segmentation" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2023/02/DL0-md.jpg" alt="AI Assisted Tool for CryoEM Segmentation"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/ai-assisted-tool-for-cryoem-segmentation" title="AI Assisted Tool for CryoEM Segmentation">AI Assisted Tool for CryoEM Segmentation</a> </p> <p class="card-type"> <em><small>Demo, Data</small></em> </p> <p class="card-text text-justify"> <small>28 Nov 2022</small> - Here we provide a tutorial to interactively segment a cellular cryo-electron tomography image using the AI assisted segmentation tool of the Segmentation+ workroom. <a href="/software-em-3d-vis/xtra-library/xtras/ai-assisted-tool-for-cryoem-segmentation">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/ai-assisted-tool-for-cryoem-segmentation">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/divide-full-data-volume-into-defined-sub-volume-blocks-for-label-analysis" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2021/10/snapshot-md.jpg" alt="Divide Full Data Volume into Defined Sub-Volume Blocks for Label Analysis"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/divide-full-data-volume-into-defined-sub-volume-blocks-for-label-analysis" title="Divide Full Data Volume into Defined Sub-Volume Blocks for Label Analysis">Divide Full Data Volume into Defined Sub-Volume Blocks for Label Analysis</a> </p> <p class="card-type"> <em><small>Recipe (hxrecipe), Project (hx, pgo), Demo</small></em> </p> <p class="card-text text-justify"> <small>1 Sep 2022</small> - This Xtra demonstrates how to use the Arithmetic module to divide a whole volume data into defined sub-volume blocks and then perform label analysis on the blocks. <a href="/software-em-3d-vis/xtra-library/xtras/divide-full-data-volume-into-defined-sub-volume-blocks-for-label-analysis">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/divide-full-data-volume-into-defined-sub-volume-blocks-for-label-analysis">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-install-the-deep-learning-python-environment" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2022/07/DLInstall-md.png" alt="How to Install the Deep Learning Python Environment"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-install-the-deep-learning-python-environment" title="How to Install the Deep Learning Python Environment">How to Install the Deep Learning Python Environment</a> </p> <p class="card-type"> <em><small>Python (pyscro), Demo, Misc</small></em> </p> <p class="card-text text-justify"> <small>29 Jul 2022</small> - Two videos explain how to install the dependencies needed to use Deep Learning within Amira 3D, Avizo 3D, or Pergeos. One covers the standard install and the other is for users without an internet connection. <a href="/software-em-3d-vis/xtra-library/xtras/how-to-install-the-deep-learning-python-environment">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/how-to-install-the-deep-learning-python-environment">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-calculate-surface-area-of-a-custom-roi" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2022/07/CustomROI-md.png" alt="How to Calculate Surface Area of a Custom ROI"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-calculate-surface-area-of-a-custom-roi" title="How to Calculate Surface Area of a Custom ROI">How to Calculate Surface Area of a Custom ROI</a> </p> <p class="card-type"> <em><small>Demo, Data</small></em> </p> <p class="card-text text-justify"> <small>29 Jul 2022</small> - This tutorial elaborates how to draw a region of interest on a surface. With this ROI, you can calculate its surface area. <a href="/software-em-3d-vis/xtra-library/xtras/how-to-calculate-surface-area-of-a-custom-roi">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/how-to-calculate-surface-area-of-a-custom-roi">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-calculate-surface-area" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2022/07/SurfaceArea-md.png" alt="How to Calculate Surface Area"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-calculate-surface-area" title="How to Calculate Surface Area">How to Calculate Surface Area</a> </p> <p class="card-type"> <em><small>Demo</small></em> </p> <p class="card-text text-justify"> <small>29 Jul 2022</small> - Three approaches are shown for extracting a surface and measuring the surface area of its geometry. <a href="/software-em-3d-vis/xtra-library/xtras/how-to-calculate-surface-area">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/how-to-calculate-surface-area">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/hind-paw-bone-segmentation" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2022/04/HindPawBoneSegmentation_snapshot-md.png" alt="Bone Segmentation Workflow for Murine Hindpaw"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/hind-paw-bone-segmentation" title="Bone Segmentation Workflow for Murine Hindpaw">Bone Segmentation Workflow for Murine Hindpaw</a> </p> <p class="card-type"> <em><small>Recipe ISP, IVP, A2D, Demo, Data</small></em> </p> <p class="card-text text-justify"> <small>28 Apr 2022</small> - Semi-automatic workflow and recipe for high-throughput bone segmentation of murine hindpaw micro-CT datasets. <a href="/software-em-3d-vis/xtra-library/xtras/hind-paw-bone-segmentation">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/hind-paw-bone-segmentation">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-segment-cavities-using-the-compute-ambient-occlusion-module" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2022/04/CAO-0-md.jpg" alt="How to Segment Cavities Using the Compute Ambient Occlusion Module"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-segment-cavities-using-the-compute-ambient-occlusion-module" title="How to Segment Cavities Using the Compute Ambient Occlusion Module">How to Segment Cavities Using the Compute Ambient Occlusion Module</a> </p> <p class="card-type"> <em><small>Demo</small></em> </p> <p class="card-text text-justify"> <small>12 Apr 2022</small> - This tutorial demonstrates how to segment pores or cavities using the Compute Ambient Occlusion module. <a href="/software-em-3d-vis/xtra-library/xtras/how-to-segment-cavities-using-the-compute-ambient-occlusion-module">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/how-to-segment-cavities-using-the-compute-ambient-occlusion-module">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-perform-trabecular-and-cortical-bone-segmentation" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2022/04/bone-0-md.jpg" alt="How to Perform Trabecular and Cortical Bone Segmentation"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-perform-trabecular-and-cortical-bone-segmentation" title="How to Perform Trabecular and Cortical Bone Segmentation">How to Perform Trabecular and Cortical Bone Segmentation</a> </p> <p class="card-type"> <em><small>Demo</small></em> </p> <p class="card-text text-justify"> <small>12 Apr 2022</small> - This tutorial demonstrates how to use the Compute Ambient Occlusion module to perform the segmentation of trabecular and cortical bone, as well as of the pore space, and then how to use the Arithmetic module to aggregate those results in one label field. <a href="/software-em-3d-vis/xtra-library/xtras/how-to-perform-trabecular-and-cortical-bone-segmentation">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/how-to-perform-trabecular-and-cortical-bone-segmentation">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/slab-view" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2022/09/SlabView3-md.png" alt="Slab View"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/slab-view" title="Slab View">Slab View</a> </p> <p class="card-type"> <em><small>Python (pyscro), Project (hx, pgo)</small></em> </p> <p class="card-text text-justify"> <small>24 Feb 2022</small> - The Slab View display module allows you to display only a slab from any kind of 3D visualization. <a href="/software-em-3d-vis/xtra-library/xtras/slab-view">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/slab-view">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-use-the-surface-view-module-and-create-elaborate-surface-renderings" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2022/04/surfview2-md.jpg" alt="How to Use the Surface View Module and Create Elaborate Surface Renderings"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/how-to-use-the-surface-view-module-and-create-elaborate-surface-renderings" title="How to Use the Surface View Module and Create Elaborate Surface Renderings">How to Use the Surface View Module and Create Elaborate Surface Renderings</a> </p> <p class="card-type"> <em><small>Demo</small></em> </p> <p class="card-text text-justify"> <small>30 Dec 2021</small> - This short video demonstrates the basic use of the Surface View module, and how to combine several Surface View modules to create elaborate renderings. <a href="/software-em-3d-vis/xtra-library/xtras/how-to-use-the-surface-view-module-and-create-elaborate-surface-renderings">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/how-to-use-the-surface-view-module-and-create-elaborate-surface-renderings">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/facies-classification-from-well-logs" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2021/06/plot_profile_graphs-md.png" alt="Facies Classification from Well Logs"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/facies-classification-from-well-logs" title="Facies Classification from Well Logs">Facies Classification from Well Logs</a> </p> <p class="card-type"> <em><small>Python (pyscro), Demo</small></em> </p> <p class="card-text text-justify"> <small>3 Dec 2021</small> - Facies (rock type) classification from well logs using supervised machine learning algorithms. <a href="/software-em-3d-vis/xtra-library/xtras/facies-classification-from-well-logs">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/facies-classification-from-well-logs">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/howto-customize-amira-avizo-with-moduleextender" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2021/10/Xtra_Customize_with_moduleExtender_title-md.png" alt="How to Customize Amira-Avizo with moduleExtender"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/howto-customize-amira-avizo-with-moduleextender" title="How to Customize Amira-Avizo with moduleExtender">How to Customize Amira-Avizo with moduleExtender</a> </p> <p class="card-type"> <em><small>Tcl, Misc</small></em> </p> <p class="card-text text-justify"> <small>25 Nov 2021</small> - Are there module settings you always need to change during your daily work? This Xtra describes how you can permanently change default settings of modules in Amira-Avizo. <a href="/software-em-3d-vis/xtra-library/xtras/howto-customize-amira-avizo-with-moduleextender">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/howto-customize-amira-avizo-with-moduleextender">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/dic-image-segmentation-and-quantification" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2021/11/DIC-md.jpg" alt="Differential Interference Contrast (DIC) Image Segmentation and Quantification using Deep Learning"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/dic-image-segmentation-and-quantification" title="Differential Interference Contrast (DIC) Image Segmentation and Quantification using Deep Learning">Differential Interference Contrast (DIC) Image Segmentation and Quantification using Deep Learning</a> </p> <p class="card-type"> <em><small>Recipe (hxrecipe), Deep learning model, Demo</small></em> </p> <p class="card-text text-justify"> <small>18 Nov 2021</small> - This workflow uses deep learning to segment images obtained by Differential Interference Contrast (DIC) microscopy. Nuclei and mitochondria are segmented and counted cell per cell. <a href="/software-em-3d-vis/xtra-library/xtras/dic-image-segmentation-and-quantification">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/dic-image-segmentation-and-quantification">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/porosity-volume-fraction-analysis" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2019/10/Volume_Fraction-md.jpg" alt="Porosity Volume Fraction Analysis"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/porosity-volume-fraction-analysis" title="Porosity Volume Fraction Analysis">Porosity Volume Fraction Analysis</a> </p> <p class="card-type"> <em><small>Project (hx, pgo), Demo, Data</small></em> </p> <p class="card-text text-justify"> <small>18 Nov 2021</small> - This tutorial demonstrates the steps to quantify porosity volume fraction and distribution. <a href="/software-em-3d-vis/xtra-library/xtras/porosity-volume-fraction-analysis">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/porosity-volume-fraction-analysis">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/landmark-based-data-alignment" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2021/08/LandmarkAlign-md.png" alt="Landmark based Data Alignment"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/landmark-based-data-alignment" title="Landmark based Data Alignment">Landmark based Data Alignment</a> </p> <p class="card-type"> <em><small>Tcl, Demo</small></em> </p> <p class="card-text text-justify"> <small>18 Nov 2021</small> - This module can be used to facilitate the alignment of datasets using pairs of landmarks. The video tutorial demonstrates this technique. <a href="/software-em-3d-vis/xtra-library/xtras/landmark-based-data-alignment">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/landmark-based-data-alignment">Learn more</a> </div> </div> </div> </div> <div class="col-md-6 col-lg-4"> <div class="card card-xtra"> <a href="/software-em-3d-vis/xtra-library/xtras/inter-time-steps-recipe-player" class="featured-image"> <img class="card-img-top img-fluid lazy" data-src="/software-em-3d-vis/xtra-library/uploads/2021/09/InterTimeStepsRecipePlayer-md.png" alt="Inter Time Steps Recipe Player"> <div class="xtra-type"> <span class="badge badge-type badge-primary badge-add-on" >Add-on</span> <span class="badge badge-type badge-primary badge-how-to" >How-to</span> </div> </a> <div class="card-body"> <p class="card-title"> <a href="/software-em-3d-vis/xtra-library/xtras/inter-time-steps-recipe-player" title="Inter Time Steps Recipe Player">Inter Time Steps Recipe Player</a> </p> <p class="card-type"> <em><small>Recipe (hxrecipe), Python (pyscro), Project (hx, pgo), Demo, Data</small></em> </p> <p class="card-text text-justify"> <small>18 Nov 2021</small> - The Inter Time Steps Recipe Player module executes a two-input recipe to a specific pair of two successive time steps of a time series dataset, or to all its pairs of two successive time steps. <a href="/software-em-3d-vis/xtra-library/xtras/inter-time-steps-recipe-player">Learn more</a> </p> <div class="btn-learn-more" style="display:none"> <a class="btn btn-primary btn-sm" href="/software-em-3d-vis/xtra-library/xtras/inter-time-steps-recipe-player">Learn more</a> </div> </div> </div> </div> </div> <nav> <ul class="pagination justify-content-center"> <li class="page-item active"> <a class="page-link" href="?page=1">1</a> </li> <li class="page-item"> <a class="page-link" href="?page=2">2</a> </li> <li class="page-item"> <a class="page-link" href="?page=3">3</a> </li> <li class="page-item"> <a class="page-link" href="?page=4">4</a> </li> </ul> </nav> </div> </section> </main> <footer> <nav class="navbar navbar-light bg-light navbar-expand-lg"> <div class="container"> <span class="navbar-text"> 漏 2024 Thermo Fisher Scientific. 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