Software and Data for: Interactive delineation and quantification of anatomical structure with virtual reality

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Garkov, Dimitar; Lein, Etienne; Kielkopf, Niklas; Dullin, Christian; Klein, Karsten; Sommer, Bjorn; Jordan, Alex; Schreiber, Falk, 2025, "Software and Data for: Interactive delineation and quantification of anatomical structure with virtual reality", https://doi.org/10.18419/DARUS-4779, DaRUS, V1

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Description	This dataset contains the supplemental materials, the used tools, and the release of the software presented in the paper Interactive delineation and quantification of anatomical structure with virtual reality. The dataset is structured in the typical order of data processing: Imaging Tomographic Reconstruction Brainacle Software (Delineation, Quantification) Supplementary Figures (Analysis) For usage and installation instructions please refer to the specific metadata. Other software used in the pipeline, in particular, Syrmep Tomo Project (STP) v1.5.3, Fiji (portable, no java), NIfTI Input/Output plug-in, and 7-Zip, 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. Paper abstract A virtual environment, equipped with suitable data representations, interaction techniques, and method interfaces, can facilitate effective human-in-the-loop analytics of 3D data. Motivated by this observation, we propose Brainacle, a native editor for the interactive delineation and quantification of anatomical structures in virtual reality. We validate this in a case study, where we process the gross brain regions of 20 individual animals from six different species of African cichlid fish from the tribe Lamprologinii, endemic to Lake Tanganyika in Africa. The software presented in this article can be used to quickly visualise and obtain an overview of imaged animal tissues, visually communicate features of interest, interactively add delineations, and perform different measurements in the same 3D environment. Brainacle is made available free of charge at https://brainacle.org and on the research data repository DaRUS.
Subject	Computer and Information Science
Keyword	Application Software, Virtual Reality, Pipeline, Microscopic Anatomy, Visualization, Anatomical Delineation, Quantification, Brain--Imaging, Cichlids, ELETTRA
Related Publication	Is Supplement To: Dimitar Garkov, Etienne Lein, Niklas Kielkopf, Christian Dullin, Karsten Klein, Bjorn Sommer, Alex Jordan, Falk Schreiber. Brainacle: Interactive delineation and quantification of anatomical structures with virtual reality. (submitted)
Notes	Installation 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. Ethics approval 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.
License/Data Use Agreement	Custom Dataset Terms

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	N_Multi_8_180.tdf 1. Imaging/Hierarchical Data Format - 8.3 GB Published Jun 11, 2025 6 Downloads MD5: 17a8463cd8bd77b1e9831c8afbeb18e6 An example TDF file obtained after imaging	Preview "1. Imaging/N_Multi_8_180.tdf" Access File File Access Public Download Options Hierarchical Data Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX Download Auxiliary Files XML from NetCDF/HDF5 (NcML) NcML (0.1)
	Tissue_Embedding_Protocol.rtf 1. Imaging/Rich Text Format - 7.7 KB Published Jun 11, 2025 6 Downloads MD5: c24fdf932112ce5169ca3a2f50b9421d The protocol using in the tissue embedding of the samples	Access File File Access Public Download Options Rich Text Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	N_Multi_8_180_corr_phrt.zip 2. Tomographic Reconstruction/ZIP Archive - 16.2 GB Published Jun 11, 2025 5 Downloads MD5: e61eeb632022e0cebdabcd74de078a88 An example image sequence obtained after reconstruction	Preview "2. Tomographic Reconstruction/N_Multi_8_180_corr_phrt.zip" Access File File Access Public Download Options ZIP Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	Reconstruction_Protocol_STP.pdf 2. Tomographic Reconstruction/Adobe PDF - 115.6 KB Published Jun 11, 2025 14 Downloads MD5: 126e03f72fa300a433a71b37e3779158 Processing steps and parameters for the reconstruction with STP v1.5.3	Preview "2. Tomographic Reconstruction/Reconstruction_Protocol_STP.pdf" Access File File Access Public Download Options Adobe PDF Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	Brainacle.7z 3. Brainacle/Compressed Archive - 31.1 MB Published Jun 11, 2025 8 Downloads MD5: 56c8698b29c1b94b17d0ab46b2625e52 Brainacle v1.0	Access File File Access Public Download Options Compressed Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	BrainacleJ-0.5.0.jar 3. Brainacle/application/java-archive - 48.4 KB Published Jun 11, 2025 7 Downloads MD5: 071badfee7646059973c9b3f40a59784 An ImageJ plugin to support the export of isosurface meshes to Brainacle	Access File File Access Public Download Options application/java-archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	ImageJMacros.zip 3. Brainacle/ZIP Archive - 1.4 KB Published Jun 11, 2025 5 Downloads MD5: 69355ea68ad0817fd873491ab91d81ff Contains: an installer macro for autorun, and two macros for the import and export of coordinates from and to Brainacle. For instructions see Metadata.	Preview "3. Brainacle/ImageJMacros.zip" Access File File Access Public Download Options ZIP Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	ImageJ_Preparation_(Volume_visualisation).pdf 3. Brainacle/Adobe PDF - 56.7 KB Published Jun 11, 2025 14 Downloads MD5: 30eb4d3cc627fc675c44c25690412270 Steps to prepare an image sequence in ImageJ for volume visualisation in Brainacle	Preview "3. Brainacle/ImageJ_Preparation_(Volume_visualisation).pdf" Access File File Access Public Download Options Adobe PDF Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	N_Multi_8_180.nii.zip 3. Brainacle/ZIP Archive - 206.3 MB Published Jun 11, 2025 12 Downloads MD5: 2fc7b880c94319043cca4dec41238dba Example data for Brainacle	Preview "3. Brainacle/N_Multi_8_180.nii.zip" Access File File Access Public Download Options ZIP Archive Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	Volume-Volume Correlations.png 4. Supplementary Figures/PNG Image - 42.3 KB Published Jun 11, 2025 13 Downloads MD5: d7fdd93410b4182a35946b95b5945ef7 The figure referenced in the paper, showing the correlations between the two methods for each gross brain region.	Preview "4. Supplementary Figures/Volume-Volume Correlations.png" Access File File Access Public Download Options PNG Image Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX

Citation Metadata

Persistent Identifier	doi:10.18419/DARUS-4779
Publication Date	2025-06-11
Title	Software and Data for: Interactive delineation and quantification of anatomical structure with virtual reality
Alternative URL	https://brainacle.org
Author	https://ror.org/0546hnb39https://orcid.org/0000-0002-2134-1686 https://ror.org/026stee22https://orcid.org/0000-0003-2985-0204 https://ror.org/0546hnb39https://orcid.org/0009-0009-6927-699X https://ror.org/03av75f26https://orcid.org/0000-0003-4297-8077 https://ror.org/0546hnb39https://orcid.org/0000-0002-8345-5806 https://ror.org/01egahc47https://orcid.org/0000-0003-1514-9898 https://ror.org/026stee22https://orcid.org/0000-0001-6131-9734 https://ror.org/0546hnb39https://orcid.org/0000-0002-9307-3254
Point of Contact	Use email button above to contact. Garkov, DimitarUniversity of Konstanz Schreiber, FalkUniversity of Konstanz
Description	This dataset contains the supplemental materials, the used tools, and the release of the software presented in the paper Interactive delineation and quantification of anatomical structure with virtual reality. The dataset is structured in the typical order of data processing: Imaging Tomographic Reconstruction Brainacle Software (Delineation, Quantification) Supplementary Figures (Analysis) For usage and installation instructions please refer to the specific metadata. Other software used in the pipeline, in particular, Syrmep Tomo Project (STP) v1.5.3, Fiji (portable, no java), NIfTI Input/Output plug-in, and 7-Zip, 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. Paper abstract A virtual environment, equipped with suitable data representations, interaction techniques, and method interfaces, can facilitate effective human-in-the-loop analytics of 3D data. Motivated by this observation, we propose Brainacle, a native editor for the interactive delineation and quantification of anatomical structures in virtual reality. We validate this in a case study, where we process the gross brain regions of 20 individual animals from six different species of African cichlid fish from the tribe Lamprologinii, endemic to Lake Tanganyika in Africa. The software presented in this article can be used to quickly visualise and obtain an overview of imaged animal tissues, visually communicate features of interest, interactively add delineations, and perform different measurements in the same 3D environment. Brainacle is made available free of charge at https://brainacle.org and on the research data repository DaRUS.
Subject	Computer and Information Science
Keyword	Application Software http://id.loc.gov/authorities/subjects/sh90001980 (LCSH) Virtual Reality http://id.loc.gov/authorities/subjects/sh92000880 (LCSH) Pipeline http://www.wikidata.org/entity/Q1192422 (Wikidata) Microscopic Anatomy http://id.loc.gov/authorities/subjects/sh85061084 (LCSH) Visualization http://id.loc.gov/authorities/subjects/sh85143939 (LCSH) Anatomical Delineation http://uri.interlex.org/tgbugs/uris/readable/atlas/Delineation (EDAM) Quantification http://www.wikidata.org/entity/Q12769938 (Wikidata) Brain--Imaging http://id.loc.gov/authorities/subjects/sh2008117487 (LCSH) Cichlids http://id.loc.gov/authorities/subjects/sh85025926 (LCSH) ELETTRA http://www.wikidata.org/entity/Q3717376 (Wikidata)
Topic Classification	Image and Language Processing, Computer Graphics and Visualisation, Human Computer Interaction, Ubiquitous and Wearable Computing (DFGFO) https://w3id.org/dfgfo/2024/443-05 Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions (DFGFO) https://w3id.org/dfgfo/2024/213-03
Related Publication	Is Supplement To: Dimitar Garkov, Etienne Lein, Niklas Kielkopf, Christian Dullin, Karsten Klein, Bjorn Sommer, Alex Jordan, Falk Schreiber. Brainacle: Interactive delineation and quantification of anatomical structures with virtual reality. (submitted)
Notes	Installation 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. Ethics approval 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.
Language	English
Project	SFB/Transregio 161
Funding Information	DFG: 251654672 DFG: EXC 2117 - 422037984 Max-Planck-Gesellschaft zur Förderung der Wissenschaften e. V.: Max Planck Institute of Animal Behaviour Elettra Sincrotrone Trieste: ELETTRA: 2017009, beamline SYRMEP (SYnchrotron Radiation for MEdical Physics)
Depositor	Garkov, Dimitar
Deposit Date	2025-02-17
Software	Syrmep Tomo Project, Version: 1.5.3 Fiji, Version: various Unity, Version: 2020.2.7 Brainacle, Version: 1.0 7-Zip, Version: 24.09
Related Dataset	The imaged brain scans and absolute brain sizes referenced in the paper may be obtained upon reasonable request from Alex Jordan (ajordan[at]ab.mpg.de).

Life Sciences Metadata

Organism	Other
Other Organism	Neolamprologus multifasciatus, tribe Lamprologinii; Neolamprologus brevis, tribe Lamprologinii; Lamprologus ocellatus, tribe Lamprologinii; Lamprologus callipterus, tribe Lamprologinii; Telmatochromis temporalis, tribe Lamprologinii; Lamprologus ornatipinnis, tribe Lamprologinii
Measurement Type	histology
Technology Type	Other
Other Technology Type	Imaging: Synchrotron micro-computed tomography

Software Metadata (CodeMeta v2.0)

Software Version	v1.0
Development Status	Active
Application Category	Visualization, interactive delineation and quantification with virtual reality
Application Subcategory	Research software
Programming Language	C# and HLSL used with the Unity platform
Operating Systems	Windows
Target Product	VR devices, connected to a PC
Build Instructions	https://brainacle.org#installation
Software Requirements	7-Zip https://www.7-zip.org SteamVR https://partner.steamgames.com/doc/features/steamvr/enterprise
Software Suggestions	Fiji or ImageJ
Software Help/Documentation	https://brainacle.org

Privacy Metadata

Personal Data	no

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Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom Dataset Terms - the following Custom Dataset Terms have been defined for this dataset.

The research data in this dataset is licensed under CC BY 4.0.
Use of the Brainacle research software in this dataset is permitted free of charge. Some restrictions are listed in the field Restrictions.
The BrainacleJ research software, as well as any of the ImageJ macros, in this dataset are licensed under GPL v3. The source code of BrainacleJ is available from the point of contact.

Restrictions

By installing, copying or otherwise using the Brainacle research software, any user(s) agree not to sell, rent, lease, sublicense, modify, decompile, disassemble, or reverse engineer the software or parts of it, except and only to the extent permitted by applicable law. The software is provided "AS IS" without warranty of any kind.

Citation Requirements

If you use Brainacle in your research, please also cite:

Garkov, Dimitar; Lein, Etienne; Kielkopf, Niklas; Dullin, Christian; Klein, Karsten; Sommer, Bjorn; Jordan, Alex; Schreiber, Falk, 2026, "Brainacle: Interactive delineation and quantification of anatomical structures with virtual reality" (submitted).

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Any use of the research software in this dataset, including but not limited to training AI models, is subject to the restrictions and/or the software licenses listed above.

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License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom terms specific to this dataset Custom Dataset Terms - the following Custom Dataset Terms have been defined for this dataset.

Terms of UseThe research data in this dataset is licensed under CC BY 4.0.
Use of the Brainacle research software in this dataset is permitted free of charge. Some restrictions are listed in the field Restrictions.
The BrainacleJ research software, as well as any of the ImageJ macros, in this dataset are licensed under GPL v3. The source code of BrainacleJ is available from the point of contact.

RestrictionsBy installing, copying or otherwise using the Brainacle research software, any user(s) agree not to sell, rent, lease, sublicense, modify, decompile, disassemble, or reverse engineer the software or parts of it, except and only to the extent permitted by applicable law. The software is provided "AS IS" without warranty of any kind.

Citation RequirementsIf you use Brainacle in your research, please also cite:

Garkov, Dimitar; Lein, Etienne; Kielkopf, Niklas; Dullin, Christian; Klein, Karsten; Sommer, Bjorn; Jordan, Alex; Schreiber, Falk, 2026, "Brainacle: Interactive delineation and quantification of anatomical structures with virtual reality" (submitted).

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Curation Status History

Status	Date	Assigner
	2026-10-02 09:12:45	Lisa Bagdenand
In Review by FoKUS	2026-09-28 08:31:28	Dataverse Admin

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