Visualizing Volumetric and Segmentation Data Using Mol* Volumes & Segmentations 2.0
CURRENT PROTOCOLS（2024）
Masaryk Univ
Abstract
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. (c) 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: VSToolkit-setting up and visualizing a user-constructed Mol* VS 2.0 database entryBasic Protocol 2: VSToolkit-visualizing multiple time frames and volume channelsSupport Protocol 1: Example: Adding database entry idr-13457537Alternate Protocol 1: Local-server-and-viewer-visualizing multiple time frames and volume channelsSupport Protocol 2: Addition of database entry custom-tubhiswtBasic Protocol 3: VSToolkit-visualizing a specific channel and time frameBasic Protocol 4: VSToolkit-visualizing geometric segmentationBasic Protocol 5: VSToolkit-visualizing lattice segmentationsAlternate Protocol 2: "Local-server-and-viewer"-visualizing lattice segmentationsBasic Protocol 6: "Local-server-and-viewer"-visualizing multiple volume channelsSupport Protocol 3: Deploying a server APISupport Protocol 4: Hosting Mol* viewer with VS extension 2.0Support Protocol 5: Example: Addition of database entry empiar-11756Support Protocol 6: Example: Addition of database entry emd-1273Support Protocol 7: Editing annotationsSupport Protocol 8: Addition of database entry idr-5025553
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Key words
3D visualization tools,annotation data,large-scale datasets,segmentation data,volumetric data
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