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. 2023 Jul 5;51(W1):W326-W330.
doi: 10.1093/nar/gkad411.

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations

Aliaksei Chareshneu  1 , Adam Midlik  1   2 , Crina-Maria Ionescu  1 , Alexander Rose  3 , Vladimír Horský  1   2 , Alessio Cantara  1   2 , Radka Svobodová  1   2 , Karel Berka  4 , David Sehnal  1   2
Affiliations

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations

Aliaksei Chareshneu et al. Nucleic Acids Res. .

Abstract

Segmentation helps interpret imaging data in a biological context. With the development of powerful tools for automated segmentation, public repositories for imaging data have added support for sharing and visualizing segmentations, creating the need for interactive web-based visualization of 3D volume segmentations. To address the ongoing challenge of integrating and visualizing multimodal data, we developed Mol* Volumes and Segmentations (Mol*VS), which enables the interactive, web-based visualization of cellular imaging data supported by macromolecular data and biological annotations. Mol*VS is fully integrated into Mol* Viewer, which is already used for visualization by several public repositories. All EMDB and EMPIAR entries with segmentation datasets are accessible via Mol*VS, which supports the visualization of data from a wide range of electron and light microscopy experiments. Additionally, users can run a local instance of Mol*VS to visualize and share custom datasets in generic or application-specific formats including volumes in .ccp4, .mrc, and .map, and segmentations in EMDB-SFF .hff, Amira .am, iMod .mod, and Segger .seg. Mol*VS is open source and freely available at https://molstarvolseg.ncbr.muni.cz/.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Mol*VS architecture and workflow.
Figure 2.
Figure 2.
Visualization of segmentation data via Mol*VS. The VS extension can be accessed through the Load Volume & Segmentation tab in the Mol* Viewer UI. Segment annotations are shown both in the UI and in the 3D scene.
Figure 3.
Figure 3.
Showcase of Mol*VS visualization capabilities ranging from atomic to cellular scale. (A) 3D reconstruction of a large bacteriophage based on cryo-EM and crystallographic data with assembly symmetry axes, where the segmentation distinguishes macromolecular assemblies of its major capsid protein (EMD-1014 (27)). (B) Concomitant display of two segmentation outcomes (manual and automated) for a dataset from cryo-EM combined with individual-particle electron tomography imaging of human plasma lipoproteins (in purple and azure) in complex with a monoclonal antibody (in green) (EMD-9094 (28)). (C) Mitochondrial reticulum in murine skeletal muscle imaged using ion beam scanning EM, where segmentation distinguishes mitochondria from other cellular structures (e.g., blood vessels highlighted in dark red) (EMPIAR-10070 (29)). (D) HeLa cells imaged using confocal microscopy (EMPIAR-10819, not published yet). In the image, the cell and background is highlighted in dark blue while the surrounding environment is green. (E) Nuclear segmentation of mouse blastocysts imaged using confocal microscopy (image 6001240 from dataset idr0062 (30)).
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