Limits...
MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data.

Moore EB, Poliakov AV, Lincoln P, Brinkley JF - BMC Bioinformatics (2007)

Bottom Line: A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products.We describe the design and implementation of the system, as well as several case studies that demonstrate its utility.Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine.

View Article: PubMed Central - HTML - PubMed

Affiliation: Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, USA. eider@u.washington.edu

ABSTRACT

Background: Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system.

Results: We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer.

Conclusion: MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine.

Show MeSH
Plotting Coordinates. Left. A surgical photograph with Cortical Stimulation Mapping (CSM) sites. Right. A cortical surface of the patient's own brain onto which we have plotted the CSM points. Veins are in blue, and provide landmarks that enable the user to more easily match the photograph with the surface than would be possible with sulci and gyri alone. Sites that have been found to be significant for language are colored green.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2099449&req=5

Figure 5: Plotting Coordinates. Left. A surgical photograph with Cortical Stimulation Mapping (CSM) sites. Right. A cortical surface of the patient's own brain onto which we have plotted the CSM points. Veins are in blue, and provide landmarks that enable the user to more easily match the photograph with the surface than would be possible with sulci and gyri alone. Sites that have been found to be significant for language are colored green.

Mentions: Another feature of the system allows the user to indicate the 3-D locations of cortical landmarks on a displayed brain surface, in the process generating the XML map file described earlier. In our own work we use this feature to visually (i.e. by "eye") map the locations of labels from a surgical photograph (Figure 5, left) onto a 3-D surface rendering of the patient's own brain (Figure 5, right) [29]. The labels on the photograph show the locations where areas of exposed cortex were electrically simulated during a procedure called Cortical Stimulation Mapping (CSM) [30], which is used during neurosurgery to map the locations of language-sensitive cortex. By mapping these CSM sites to the patient's own brain and later to a normalized brain atlas we can relate them to other brain mapping data such as fMRI or single unit recording (SUR) [31].


MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data.

Moore EB, Poliakov AV, Lincoln P, Brinkley JF - BMC Bioinformatics (2007)

Plotting Coordinates. Left. A surgical photograph with Cortical Stimulation Mapping (CSM) sites. Right. A cortical surface of the patient's own brain onto which we have plotted the CSM points. Veins are in blue, and provide landmarks that enable the user to more easily match the photograph with the surface than would be possible with sulci and gyri alone. Sites that have been found to be significant for language are colored green.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2099449&req=5

Figure 5: Plotting Coordinates. Left. A surgical photograph with Cortical Stimulation Mapping (CSM) sites. Right. A cortical surface of the patient's own brain onto which we have plotted the CSM points. Veins are in blue, and provide landmarks that enable the user to more easily match the photograph with the surface than would be possible with sulci and gyri alone. Sites that have been found to be significant for language are colored green.
Mentions: Another feature of the system allows the user to indicate the 3-D locations of cortical landmarks on a displayed brain surface, in the process generating the XML map file described earlier. In our own work we use this feature to visually (i.e. by "eye") map the locations of labels from a surgical photograph (Figure 5, left) onto a 3-D surface rendering of the patient's own brain (Figure 5, right) [29]. The labels on the photograph show the locations where areas of exposed cortex were electrically simulated during a procedure called Cortical Stimulation Mapping (CSM) [30], which is used during neurosurgery to map the locations of language-sensitive cortex. By mapping these CSM sites to the patient's own brain and later to a normalized brain atlas we can relate them to other brain mapping data such as fMRI or single unit recording (SUR) [31].

Bottom Line: A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products.We describe the design and implementation of the system, as well as several case studies that demonstrate its utility.Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine.

View Article: PubMed Central - HTML - PubMed

Affiliation: Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, USA. eider@u.washington.edu

ABSTRACT

Background: Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system.

Results: We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer.

Conclusion: MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine.

Show MeSH