![Patch Extraction Tools for Deep Learning Data Preparation](/software-em-3d-vis/xtra-library/uploads/2021/02/ExtractPatches_Snapshot2-md.png)
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
![Efficient Graph-based 2D Image Segmentation](/software-em-3d-vis/xtra-library/uploads/2021/01/2021-01-15 12_39_25-Amira - GraphBasedSegmentation_volumescope.hx-md.png)
Efficient Graph-based 2D Image Segmentation
XPand module
12 Feb 2021 - This Xtra implements efficient graph-based image segmentation by Felzenszwalb and Huttenlocher. Learn more
Python (pyscro)
22 Jan 2021 - This Python script-object allows you to convert a point-cloud object to a spreadsheet object. Learn more
![FIBSEM Mitochondria Segmentation](/software-em-3d-vis/xtra-library/uploads/2020/11/FIBSEM_Mitochondria_Segmentation_zoom-md.jpg)
FIBSEM Mitochondria Segmentation
Deep learning model
12 Jan 2021 - Pre-trained model for the Deep Learning Prediction module detecting mitochondria in a Focused Ion Beam Scanning Electron Microscope (FIBSEM) data set. Learn more
![Multi-Component Analysis of X-ray Computed Tomography Datasets](/software-em-3d-vis/xtra-library/uploads/2020/11/image-md.jpg)
Multi-Component Analysis of X-ray Computed Tomography Datasets
Recipe (hxrecipe), Project (hx, pgo), Demo, Data, Misc
4 Jan 2021 - The following videos and training material detail the steps taken to automate the analysis of multiple parts in a single X-ray CT volume. Learn more
![Thresholding From Mean](/software-em-3d-vis/xtra-library/uploads/2020/12/thresholdingFromMean-2-md.png)
Python (pyscro), Data
4 Jan 2021 - This module performs an adaptive global thresholding of the input image by computing a deviation from the mean of its grayscale values. Learn more
Tcl
17 Nov 2020 - This module creates a spreadsheet that contains the measurement and annotation data (generated with the Measurement tool) that can be used for further analysis. Learn more
![Marker Based Watershed Recipe](/software-em-3d-vis/xtra-library/uploads/2020/10/snapshot-md.png)
Recipe ISP, IVP, A2D
17 Nov 2020 - A recipe for applying a Marker Based Watershed (as in the Segmentation Editor) from the Project View. Learn more
![Automatic Extraction of Transparent Surface Cross Section](/software-em-3d-vis/xtra-library/uploads/2020/10/Xtra-extractXsection-md.png)
Automatic Extraction of Transparent Surface Cross Section
Python (pyscro), Project (hx, pgo)
20 Oct 2020 - A module for creating partially transparent capping surfaces. Learn more
Auto Threshold for Multi-Thresholding
Tcl
19 Oct 2020 - The combination of Auto Thresholding and Multi-Thresholding makes it easy to create precise surfaces without additional smoothing, using the Generate Surface's smoothing option "Existing Weights". Learn more
![Volume Projection](/software-em-3d-vis/xtra-library/uploads/2020/09/snapshotVolumeProjection-md.png)
Python (pyscro)
19 Oct 2020 - This Xtra creates a volume projection along any orthogonal axis using arithmetic operations. Learn more
![Relative Area Fraction for Amira-Avizo2D](/software-em-3d-vis/xtra-library/uploads/2020/10/HowTo_RelativeAreaFraction-md.jpg)
Relative Area Fraction for Amira-Avizo2D
Recipe ISP, IVP, A2D, Python (pyscro), Data, Misc
5 Oct 2020 - This Xtra provides a module to help compute the area fraction of a label over the area of another label in Amira-Avizo2D. Learn more
![Explode Surface Animation Script](/software-em-3d-vis/xtra-library/uploads/2020/07/ExplodeSurface2-md.png)
Explode Surface Animation Script
Tcl
5 Oct 2020 - A script that will animate the expansion of pieces of a surface. Contains the script, documentation, an example surface, and a video of the finished result. Learn more
![Apply a Recipe on a Batch of Files](/software-em-3d-vis/xtra-library/uploads/2022/03/3-8-2022 10-39-58 AM-md.jpg)
Apply a Recipe on a Batch of Files
Recipe (hxrecipe), Tcl
25 Aug 2020 - Apply a recipe to a batch of files and save the results in an output directory. Learn more
![Selective Border Kill](/software-em-3d-vis/xtra-library/uploads/2020/07/snapshot_selectiveborderkill-md.jpg)
Tcl
24 Aug 2020 - A module that allows you to filter particles selectively, based on their contact with each border of the image. Learn more
![Segmentation of agglomerated Ni nanoparticles](/software-em-3d-vis/xtra-library/uploads/2019/10/size-distribution-Ni-md.jpg)
Segmentation of agglomerated Ni nanoparticles
Recipe ISP, IVP, A2D
24 Aug 2020 - This recipe segments overlapping Ni nanoparticles on a high resolution STEM image. A size distribution of the nanoparticles can also be computed. Learn more
![Hough Circle Fitting](/software-em-3d-vis/xtra-library/uploads/2023/03/hough circle fitting xtra-md.png)
Python (pyscro)
30 Jul 2020 - This module uses a Generalized Hough-transform to detect circles in an image. Learn more
![Multi-Scale Cylinder Correlation](/software-em-3d-vis/xtra-library/uploads/2020/04/MultiScaleCylinderCorrelation-md.png)
Multi-Scale Cylinder Correlation
Python (pyscro), Project (hx, pgo)
30 Jul 2020 - This module gives better results for fiber-tracing in the case of multiple fibers with differing or varying diameters in the same dataset. Learn more
![Cylinder Slice with Native Resolution in Z](/software-em-3d-vis/xtra-library/uploads/2022/02/2-25-2022 3-08-16 PM-md.jpg)
Cylinder Slice with Native Resolution in Z
XPand module
10 Jul 2020 - This Xtra module is a version of the Cylinder Slice module that sets the resolution, in the Z direction, of the extracted image to the native resolution of the input data. Learn more
![Optical Thin Section Pore Space Characterization in HSV colorspace](/software-em-3d-vis/xtra-library/uploads/2020/02/Xtra-image_HSV_threshold-md.jpg)
Optical Thin Section Pore Space Characterization in HSV colorspace
Python (pyscro), Project (hx, pgo), Data
10 Jul 2020 - Optical Thin Section Pore Space is segmented converting RGBA images in HSV colorspace by means of Python scripts. Learn more
![Segment TEM data without artifact and background effect](/software-em-3d-vis/xtra-library/uploads/2020/07/Xtra_TEM-md.png)
Segment TEM data without artifact and background effect
Recipe (hxrecipe), Tcl, Project (hx, pgo)
10 Jul 2020 - Segment TEM data aided by the Structure enhancement filter. Learn more