Slice by Slice Thinning
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Slice by Slice Thinning

XPand module

6 Apr 2022 - This module performs the thinning of a binary image slice-by-slice.  Learn more

Slab View
Add-on How-to

Slab View

Python (pyscro), Project (hx, pgo)

24 Feb 2022 - The Slab View display module allows you to display only a slab from any kind of 3D visualization.  Learn more

How to Customize Amira-Avizo with moduleExtender
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How to Customize Amira-Avizo with moduleExtender

Tcl, Misc

25 Nov 2021 - 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.  Learn more

Masking Map by Molecule
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Masking Map by Molecule

Tcl

18 Nov 2021 - Module Mask Map By Molecule lets you mask an EM map of a macro molecule by an atomic model of the entire or partial molecule. This can be useful when validating EM maps from SPA with published models from the Protein Data Bank.  Learn more

kMeans Clustering on Label Analysis (Python)
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kMeans Clustering on Label Analysis (Python)

Python (pyscro)

18 Nov 2021 - This Xtra implements kMeans clustering on a label analysis spreadsheet. Separated objects can be clustered based on any measure group that is inbuilt or user customized.  Learn more

Differential Interference Contrast (DIC) Image Segmentation and Quantification using Deep Learning
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Differential Interference Contrast (DIC) Image Segmentation and Quantification using Deep Learning

Recipe (hxrecipe), Deep learning model, Demo

18 Nov 2021 - 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.  Learn more

Porosity Volume Fraction Analysis
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Porosity Volume Fraction Analysis

Project (hx, pgo), Demo, Data

18 Nov 2021 - This tutorial demonstrates the steps to quantify porosity volume fraction and distribution.  Learn more

Bookmarks Manager
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Bookmarks Manager

Python (pyscro)

18 Nov 2021 - Add bookmarks to your project, including status and camera, so you can easily retrieve a given visualization. You can then navigate through the bookmarks.  Learn more

Landmark based Data Alignment
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Landmark based Data Alignment

Tcl, Demo

18 Nov 2021 - This module can be used to facilitate the alignment of datasets using pairs of landmarks. The video tutorial demonstrates this technique.  Learn more

Inter Time Steps Recipe Player
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Inter Time Steps Recipe Player

Recipe (hxrecipe), Python (pyscro), Project (hx, pgo), Demo, Data

18 Nov 2021 - 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.  Learn more

How to Script the Instantiation of a Python Script Object Xtra
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How to Script the Instantiation of a Python Script Object Xtra

Python (pyscro)

9 Sep 2021 - This Xtra provides a script template that can be used to instantiate a Python script object Xtra from the Python console or from a Python script.  Learn more

Using Tcl Command Module for Multi-File OBJ Export
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Using Tcl Command Module for Multi-File OBJ Export

Tcl, Project (hx, pgo)

7 Sep 2021 - The Tcl Command Module makes it easy to export the surfaces of single objects from a multi-object surface as OBJ (Wavefront) files.  Learn more

Split and Merge Segments
Add-on How-to

Split and Merge Segments

XPand module

29 Jun 2021 - The Split and Merge Segments module merges the two most representative segments at the intersection points of a graph structure and detaches the others.  Learn more

Browse TensorBoard of old Deep Learning Training sessions
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Browse TensorBoard of old Deep Learning Training sessions

Deep learning model, Python (pyscro)

21 May 2021 - This Xtra contains a module that allows you to browse TensorBoard logs from previous Deep Learning Training sessions.  Learn more

Add Data To Point Cloud
Add-on

Add Data To Point Cloud

Python (pyscro)

29 Mar 2021 - AddDataToPointCloud writes data defined on mesh-nodes into a point-cloud with an equal number of points. Together with the "PointCloudToSpreadsheet" Xtra, this module can be used, for example, to export the results created by the Surface Distance module.  Learn more

Extract Oriented Labels
Add-on How-to

Extract Oriented Labels

Python (pyscro), Project (hx, pgo)

29 Mar 2021 - The Extract Oriented Labels module extracts every label from the input label image, and resamples each image along its own main orientations (or eigenvectors).  Learn more

Fitting Molecule To Map
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Fitting Molecule To Map

Tcl

8 Mar 2021 - This Xtra contains a script module to fit molecular models to density maps, a process frequently called "docking".  Learn more

Image Segmentation Evaluation Using Standard Metrics
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Image Segmentation Evaluation Using Standard Metrics

Python (pyscro), Project (hx, pgo)

8 Mar 2021 - Segmentation evaluation using standard precision, and recall metrics for comparing two segmentation labels.  Learn more

Getting Started with Flatten Module
Add-on How-to

Getting Started with Flatten Module

Project (hx, pgo), Demo

8 Mar 2021 - This tutorial demonstrates use of the Flatten experimental module to create interactive contours by defining the unfolding surface while respecting the constraints of the module inputs.  Learn more

Large Data Visualization
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Large Data Visualization

Demo, Misc

24 Feb 2021 - This video tutorial demonstrates how to deal with visualization of large datasets.  Learn more

Patch Extraction Tools for Deep Learning Data Preparation
Add-on

Patch Extraction Tools for Deep Learning Data Preparation

Python (pyscro)

22 Feb 2021 - A set of tools dedicated to the preparation of data for training Deep Learning models and reducing annotation time.  Learn more