AAFS2021

This repository contains supplemental material for my poster at the American Academy of Forensic Sciences 2021 virtual meeting, #A49, “3D Web-Based Technologies to Support Interactive Forensic Anthropology Databases.”

Section Links:

3DHOP Three.js VTK.js OpenAnatomy XTK Sketchfab RShiny Summary References

Example Data

Below are brief descriptions of the resources discussed in the poster, along with links to the examples.

3DHOP

Customized 3DHOP examples are provided to demonstrate single model viewing and multiple model viewing, with features such as transparency, multi-plane cross-sectioning, model color adjustments, anatomical views, landmarking, and measurements. Model color picker was added using jscolor.js.

3dhop_multipart

Example models include:

Included models are in PLY format. Large file sizes (such as microCT) may be compressed to a NXS or NXZ format.

*Skull models were generated from the Head-Neck_Cetuximab collection under National Institute of Justice grant #2014-DN-BX-K005.*

*Models in medlymph006 folder are preliminary models generated for demonstration purposes using CT data from the CT Lymph Nodes collection of the Cancer Imaging Archive.* See References for full citations.

Three.js

A GLTF file is provided for viewing with the GLTF viewer located here (drop GLTF into browser window). Source code.

gltf viewer

The GLTF file was generated by exporting a multi-part segmentation hierarchy from 3D Slicer using the OpenAnatomy module:

OpenAnatomy module --> Segmentation Export --> GLTF (selecting the segmentation hierarchy).

VTK.js

A VTI file is provided for viewing with the Volume Viewer located here (drop VTI into browser window). This resource provides a way to view and interact with a de-identified 3D CT volume without needing to generate 3D surface models.

vti volume viewer

The VTI was generated by exporting a CT volume (after importing a DICOM series that had been saved as a NRRD volume) from 3D Slicer using the OpenAnatomy module:

OpenAnatomy module --> Image Export --> VTI.

The Volume Viewer file can be downloaded and used offline to load and display a local VTI file.

*The provided VTI was generated with CT scan TC634 collected by Lynn Copes from the Terry Collection at the National Museum of Natural History, Washington, D.C.*

OpenAnatomy

The Open Anatomy project provides viewing of CT volumes, segmentations, and 3D models in order to facilitate multi-modal interaction with anatomy atlases or scenes. Exports a segmentation/model hierarchy as a GLTF or a CT volume as a VTI from the OpenAnatomy module in 3D Slicer.

open anatomy module exports

XTK

The X toolkit can accomodate CT volumes as well as 3D models. An example NRRD volume is provided to demonstrate the Slice:Drop viewer. NRRD volume was generated from the Visible Human Female downloaded from https://mri.radiology.uiowa.edu/visible_human_datasets.html.

xtk slice drop

Sketchfab

Sketchfab can accept multiple model files, including GLTF scenes as demonstrated here.

Model viewers on Sketchfab can be embedded in external web pages by anyone, even without a Sketchfab account, by copying the </> Embed code into an HTML document, for example, to generate study sets for students.

Additional features for the viewers require upgraded accounts.

Example

sketchfab_page

RShiny

HTML documents that contain 3D data can be attached to R Shiny applications by installing libraries (shiny, rgl, htmltools, htmlwidgets) and directing the application to the HTML page.

For existing applications developed for forensic anthropology, this means 3D HTML pages can be “attached” to provide access to reference datasets or example models. To test this, the provided 3DHOP examples could be used by placing the entire directory inside a “www” folder after starting an R Studio project and directing the code in the below image to one of the HTML pages (index.html can be used and the relative links to the additional pages will be retained)

shiny 3D html

Summary

References

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