Visualizing Volumetric and Segmentation Data using Mol* Volumes
& Segmentations 2.0

J 2024

Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0

CHARESHNEU, Aliaksei; Alessio CANTARA; Dominik TICHY a David SEHNAL

Základní údaje

Originální název

Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0

Autoři

CHARESHNEU, Aliaksei; Alessio CANTARA; Dominik TICHY a David SEHNAL

Vydání

Current Protocols, Wiley, 2024, 2691-1299

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.200

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/24:00138951

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

3D visualization tools; annotation data; large-scale datasets; segmentation data; volumetric data

Štítky

143160, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 28. 2. 2025 16:27, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

Ever-increasing availability of experimental volumetric data (e.g., in .ccp4, .mrc, .map, .rec, .zarr, .ome.tif formats) and advances in segmentation software (e.g., Amira, Segger, IMOD) and formats (e.g., .am, .seg, .mod, etc.) have led to a demand for efficient web-based visualization tools. Despite this, current solutions remain scarce, hindering data interpretation and dissemination. Previously, we introduced Mol* Volumes & Segmentations (Mol* VS), a web application for the visualization of volumetric, segmentation, and annotation data (e.g., semantically relevant information on biological entities corresponding to individual segmentations such as Gene Ontology terms or PDB IDs). However, this lacked important features such as the ability to edit annotations (e.g., assigning user-defined descriptions of a segment) and seamlessly share visualizations. Additionally, setting up Mol* VS required a substantial programming background. This article presents an updated version, Mol* VS 2.0, that addresses these limitations. As part of Mol* VS 2.0, we introduce the Annotation Editor, a user-friendly graphical interface for editing annotations, and the Volumes & Segmentations Toolkit (VSToolkit) for generating shareable files with visualization data. The outlined protocols illustrate the utilization of Mol* VS 2.0 for visualization of volumetric and segmentation data across various scales, showcasing the progress in the field of molecular complex visualization.

Návaznosti

GM22-30571M, projekt VaV

Název: Cell*: webová platforma pro vizualizaci, modelování a dynamiku organelových a buněčných struktur (Akronym: Cell*)

Investor: Grantová agentura ČR, Cell*: a web platform for visualization, modelling and dynamics of organelle- and cell-sized structures

Citovat

CHARESHNEU, Aliaksei; Alessio CANTARA; Dominik TICHY a David SEHNAL. Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0. Current Protocols. Wiley, 2024, roč. 4, č. 12, s. 1-34. ISSN 2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.70070.

@article{2480597,
   author = {Chareshneu, Aliaksei and Cantara, Alessio and Tichy, Dominik and Sehnal, David},
   article_number = {12},
   doi = {https://doi.org/10.1002/cpz1.70070},
   keywords = {3D visualization tools; annotation data; large-scale datasets; segmentation data; volumetric data},
   language = {eng},
   issn = {2691-1299},
   journal = {Current Protocols},
   title = {Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0},
   url = {https://doi.org/10.1002/cpz1.70070},
   volume = {4},
   year = {2024}
}

TY  - JOUR
ID  - 2480597
AU  - Chareshneu, Aliaksei - Cantara, Alessio - Tichy, Dominik - Sehnal, David
PY  - 2024
TI  - Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0
JF  - Current Protocols
VL  - 4
IS  - 12
SP  - 1-34
EP  - 1-34
PB  - Wiley
SN  - 26911299
KW  - 3D visualization tools
KW  - annotation data
KW  - large-scale datasets
KW  - segmentation data
KW  - volumetric data
UR  - https://doi.org/10.1002/cpz1.70070
N2  - Ever-increasing availability of experimental volumetric data (e.g., in .ccp4, .mrc, .map, .rec, .zarr, .ome.tif formats) and advances in segmentation software (e.g., Amira, Segger, IMOD) and formats (e.g., .am, .seg, .mod, etc.) have led to a demand for efficient web-based visualization tools. Despite this, current solutions remain scarce, hindering data interpretation and dissemination. Previously, we introduced Mol* Volumes & Segmentations (Mol* VS), a web application for the visualization of volumetric, segmentation, and annotation data (e.g., semantically relevant information on biological entities corresponding to individual segmentations such as Gene Ontology terms or PDB IDs). However, this lacked important features such as the ability to edit annotations (e.g., assigning user-defined descriptions of a segment) and seamlessly share visualizations. Additionally, setting up Mol* VS required a substantial programming background. This article presents an updated version, Mol* VS 2.0, that addresses these limitations. As part of Mol* VS 2.0, we introduce the Annotation Editor, a user-friendly graphical interface for editing annotations, and the Volumes & Segmentations Toolkit (VSToolkit) for generating shareable files with visualization data. The outlined protocols illustrate the utilization of Mol* VS 2.0 for visualization of volumetric and segmentation data across various scales, showcasing the progress in the field of molecular complex visualization.
ER  -

CHARESHNEU, Aliaksei; Alessio CANTARA; Dominik TICHY a David SEHNAL. Visualizing Volumetric and Segmentation Data using Mol* Volumes \&{} Segmentations 2.0. \textit{Current Protocols}. Wiley, 2024, roč.~4, č.~12, s.~1-34. ISSN~2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.70070.

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