DOI: 10.18419/darus-4779
title: Software and Data for: Interactive delineation and quantification of anatomical structure with virtual reality

description: This dataset contains the supplemental materials, the used tools, and the release of the software presented in the paper &lt;i&gt;Interactive delineation and quantification of anatomical structure with virtual reality&lt;/i&gt;. The dataset is structured in the typical order of data processing:

&lt;ol&gt;
 &lt;li&gt;Imaging&lt;/li&gt;
 &lt;li&gt;Tomographic Reconstruction&lt;/li&gt;
 &lt;li&gt;Brainacle Software (Delineation, Quantification)&lt;/li&gt;
 &lt;li&gt;Supplementary Figures (Analysis)&lt;/li&gt;
&lt;/ol&gt;

For usage and installation instructions please refer to the specific metadata.&lt;/br&gt;&lt;/br&gt;

Other software used in the pipeline, in particular, &lt;a href="https://github.com/ElettraSciComp/STP-Gui"&gt;Syrmep Tomo Project (STP)&lt;/a&gt; v1.5.3, &lt;a href="https://fiji.sc"&gt;Fiji&lt;/a&gt; (portable, no java), &lt;a href="https://imagej.net/ij/plugins/nifti.html"&gt;NIfTI Input/Output plug-in&lt;/a&gt;, and &lt;a href="https://www.7-zip.org"&gt;7-Zip&lt;/a&gt;, may be obtained from the point of contact in the case of changes to the software or inavailability from the respective website. These have been preserved in a separate DRAFT dataset here on DaRUS.&lt;/br&gt;&lt;/br&gt; 

&lt;b&gt;Paper abstract&lt;/b&gt;&lt;br/&gt;
&lt;b&gt;Background&lt;/b&gt;&lt;br/&gt;
Full tissue segmentation is laborious, especially for non-model organisms, whereas accurate and reliable delineation still requires much firsthand visual inspection.
A virtual environment can be equipped with suitable data representations, interaction techniques, and method interfaces as to enable the interactive delineation and quantification of anatomical structure.
Situated in such an environment, analysts can benefit from reduced pre-processing, but also from in-situ learning and collaboration.&lt;br/&gt;

&lt;b&gt;Results&lt;/b&gt;&lt;br/&gt;
Therefore, we apply virtual reality as a method to visualise and derive higher-level anatomical features from low-level descriptors.
Following voxel-size calibration, scalable delineations and measurements are performed in virtual reality. 
The data representation for delineation is volume visualisation: a volume rendering or an isosurface mesh.
Two delineation techniques are proposed for the placement and editing of points and segments in virtual reality. 
For quantification, different measures and metrics can be computed for each delineated region.
To mitigate some of the fundamental challenges of virtual reality, e. g., mid-air interaction affecting precision at a distance, different virtual-reality affordances were considered as part of the design.
As a result, we present &lt;i&gt;Brainacle&lt;/i&gt;, a virtual reality application, and make its usage freely available.
We incorporate &lt;i&gt;Brainacle&lt;/i&gt; in a synchrotron tomography reconstruction pipeline to delineate and quantify the gross brain regions of 20 individuals from six species of African cichlid fish.&lt;br/&gt;

&lt;b&gt;Conclusion&lt;/b&gt;&lt;br/&gt;
&lt;i&gt;Brainacle&lt;/i&gt;, an editor for the interactive delineation and quantification of anatomical structures in virtual reality, is applicable to different biological pipelines and workflows.
In particular, &lt;i&gt;Brainacle&lt;/i&gt; can be used to quickly gain an overview of structure, ease repetitive delineation and measurement, and visually inspect and communicate findings.
description: Syrmep Tomo Project, 1.5.3
description: Fiji, various
description: Unity, 2020.2.7
description: Brainacle, 1.0
description: 7-Zip, 24.09
description: <b>Installation</b>
1) Download Brainacle on your local machine.
2) Unpack the archive file and provide the phrase brainacle version 1.0.
3) Make sure SteamVR is installed and a VR device is connected.

<b>Ethics approval</b>
In accordance with standard ethical procedures, fish were euthanized in a water bath of MS-222 dissolved in holding water, and subsequently rapidly decapitated to ensure death. The euthanasia of fish for extraction of brains was registered under file number T-17/11TFA at the responsible state authority.