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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. © 2024 The Author(s). 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引用次数: 0
Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0
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. © 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 entry
Basic Protocol 2: VSToolkit—visualizing multiple time frames and volume channels
Support Protocol 1: Example: Adding database entry idr-13457537
Alternate Protocol 1: Local-server-and-viewer—visualizing multiple time frames and volume channels
Support Protocol 2: Addition of database entry custom-tubhiswt
Basic Protocol 3: VSToolkit—visualizing a specific channel and time frame
Basic Protocol 4: VSToolkit—visualizing geometric segmentation
Basic Protocol 5: VSToolkit—visualizing lattice segmentations
Alternate Protocol 2: “Local-server-and-viewer”—visualizing lattice segmentations
Basic Protocol 6: “Local-server-and-viewer”—visualizing multiple volume channels
Support Protocol 3: Deploying a server API
Support Protocol 4: Hosting Mol* viewer with VS extension 2.0
Support Protocol 5: Example: Addition of database entry empiar-11756
Support Protocol 6: Example: Addition of database entry emd-1273
Support Protocol 7: Editing annotations
Support Protocol 8: Addition of database entry idr-5025553
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