Difference between revisions of "2007 APR NIH Questions and Answers"
From NAMIC Wiki
(/* The visualization tool allows the overlay of spherical, vector and ellipsoid data onto surfaces via versatile color maps. Is this extensible to other data, such a genetic or molecular data? ('''St) |
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==== The visualization tool allows the overlay of spherical, vector and ellipsoid data onto surfaces via versatile color maps. Is this extensible to other data, such a genetic or molecular data? ('''Steve Pieper''')==== | ==== The visualization tool allows the overlay of spherical, vector and ellipsoid data onto surfaces via versatile color maps. Is this extensible to other data, such a genetic or molecular data? ('''Steve Pieper''')==== | ||
| − | The NA-MIC Kit is a set of compatible tools including utilities, libraries, and applications. At the application level, there are many promising areas of genetic or molecular research to which 3D Slicer has not been applied. 3D Slicer is extensible though, with current active projects and pending collaboration grant proposals to adapt and enhance the application to process microscopy data. For example, Drs. Bryan Smith and Mark Ellisman of UCSD are [[2007_Project_Week_Support_for_electron_microscopy | working on this topic]] through a supplement via the NCBC program. In addition Drs. Machiraju, Pieper, Aylward, and Davis of Ohio State, Isomics, and Kitware have jointly applied for a NA-MIC collaboration grant with the goal of implementing advanced image analysis algorithms that are well adapted to detecting cellular structures (currently in review). Dr. Gouaillard of CalTech is also [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | collaborating with NA-MIC]] to adapt tools from the [http://www.cegs.caltech.edu/ Center of Excellence in Genomic Science (CEGS)] to work with their studies of the zebra fish embryogenesis. Beyond these specific examples, [http://www.na-mic.org/Wiki/index.php/Slicer:Feedback a wide range of research applications] from surgery planning to astronomy have been enabled by the software. As the slicer3 platform matures, an even larger range of applications is anticipated. At the library and utility levels an even greater diversity of applications is possible as demonstrated by [http://www.kitware.com/case/vtkinuse.html the range of applications using VTK] and [http://www.itk.org/HTML/Applications.htm the applications developed on ITK]. | + | The NA-MIC Kit is a set of compatible tools including utilities, libraries, and applications. At the application level, there are many promising areas of genetic or molecular research to which 3D Slicer has not been applied. 3D Slicer is extensible though, with current active projects and pending collaboration grant proposals to adapt and enhance the application to process microscopy data. For example, Drs. Bryan Smith and Mark Ellisman of UCSD are [[Projects/Slicer3/2007_Project_Week_Support_for_electron_microscopy | working on this topic]] through a supplement via the NCBC program. In addition Drs. Machiraju, Pieper, Aylward, and Davis of Ohio State, Isomics, and Kitware have jointly applied for a NA-MIC collaboration grant with the goal of implementing advanced image analysis algorithms that are well adapted to detecting cellular structures (currently in review). Dr. Gouaillard of CalTech is also [[NA-MIC_NCBC_Collaboration:3D%2Bt_Cells_Lineage:GoFigure | collaborating with NA-MIC]] to adapt tools from the [http://www.cegs.caltech.edu/ Center of Excellence in Genomic Science (CEGS)] to work with their studies of the zebra fish embryogenesis. Beyond these specific examples, [http://www.na-mic.org/Wiki/index.php/Slicer:Feedback a wide range of research applications] from surgery planning to astronomy have been enabled by the software. As the slicer3 platform matures, an even larger range of applications is anticipated. At the library and utility levels an even greater diversity of applications is possible as demonstrated by [http://www.kitware.com/case/vtkinuse.html the range of applications using VTK] and [http://www.itk.org/HTML/Applications.htm the applications developed on ITK]. |
Our approach to extending our software into new fields, such as the wider ranges of genetic or molecular images mentioned in the question, is to identify collaborators who need new image computing solutions of the type NA-MIC is providing. These collaborations often start through technical points of contact; programmers often research open source tools and begin 'tinkering' to see what can be re-used in a new application. If there is sufficient interest, these experiments can grow into collaboration in new fields. For example [[NA-MIC_Collaborations#PAR-05-063:_Automated_FE_Mesh_Development | the collaboration with University of Iowa on Finite Element Meshing]] applies the software in a new direction that other NA-MIC developers had not been exploring. | Our approach to extending our software into new fields, such as the wider ranges of genetic or molecular images mentioned in the question, is to identify collaborators who need new image computing solutions of the type NA-MIC is providing. These collaborations often start through technical points of contact; programmers often research open source tools and begin 'tinkering' to see what can be re-used in a new application. If there is sufficient interest, these experiments can grow into collaboration in new fields. For example [[NA-MIC_Collaborations#PAR-05-063:_Automated_FE_Mesh_Development | the collaboration with University of Iowa on Finite Element Meshing]] applies the software in a new direction that other NA-MIC developers had not been exploring. | ||
Revision as of 17:37, 3 August 2007
Home < 2007 APR NIH Questions and AnswersIn a letter from Grace Peng, dated July 31 2007 the center team asks the following questions:
Contents
- 1 The weakest and probably most difficult parts of the NA-MIC effort are validation and comparison across algorithms. The validation that is being performed needs to be more systematic and coordinated like the tractography validation effort. Perhaps methods that engage the user community could be tried. (Ross Whitaker)
- 2 To what problems is DTI best applicable? Is it applicable across age ranges?(Ross Whitaker)
- 3 Although the NA-MIC Wiki contains information on who is using the NA-MIC kit and what are they using it for, the next annual report should either summarize this information or provide a link to the information. (Tina Kapur)
- 4 The next annual report should include a link and reference to the User Manual for the NA-MIC Kit.(Will Schroeder)
- 5 What is the rational for choosing a particular method (tool) for solving a particular problem (DBP)? Why was a particular method (tool) chosen for development? Is there a listing of which tool might be helpful for which family of problems? Please provide more specific details to these questions as they have been asked previously by the Center Team. (Ross Whitaker)
- 6 A clinical project between Toronto and BWH still is recruitment phase in planning a DTI and genetic study of psychosis. What would be the genetic component? (Martha Shenton)
- 6.1 Drs. Martha Shenton (BWH) and James Kennedy (University of Toronto) are beginning a collaboration together based on mutual interests, although the specific goals have yet to be worked out. Specifically, Dr. Shenton is very much interested in developing further expertise in her laboratory in the area of genetics, particularly in area of white matter genes and their association with white matter fiber tract abnormalities evaluated using DTI in schizophrenia. Dr. Shenton has an instructor in Psychiatry at BWH who works in her laboratory who will be visiting Dr. Kennedy’s laboratory for a one week period in August of 2007, to be followed by several later visits, to learn state-of-the-art techniques used for evaluating white matter genes and their role in schizophrenia.
- 6.2 In parallel, Dr. Kennedy is very much interested in developing further expertise in his laboratory in the area of neuroimaging, particularly in both morphometry and DTI measures of white matter in schizophrenia, which he will correlate with genetic data involving white matter genes. Following up on this interest, Dr. Kennedy has a 4th year resident in psychiatry at the University of Toronto School of Medicine who works in his laboratory and who is visiting Dr. Shenton’s laboratory from July 1, 2007 to December 31, 2007, to learn state-of-the-art neuroimaging techniques including DTI and its application to understanding white matter pathology in schizophrenia. It is too early at this point to determine where this collaboration will go although it is clear that there is a tremendous amount of interest on both Dr. Shenton’s and Dr. Kennedy’s part, and the hope is that these early efforts will come to fruition in a grant that supports this collaborative endeavor.
- 7 The visualization tool allows the overlay of spherical, vector and ellipsoid data onto surfaces via versatile color maps. Is this extensible to other data, such a genetic or molecular data? (Steve Pieper)
The weakest and probably most difficult parts of the NA-MIC effort are validation and comparison across algorithms. The validation that is being performed needs to be more systematic and coordinated like the tractography validation effort. Perhaps methods that engage the user community could be tried. (Ross Whitaker)
To what problems is DTI best applicable? Is it applicable across age ranges?(Ross Whitaker)
Although the NA-MIC Wiki contains information on who is using the NA-MIC kit and what are they using it for, the next annual report should either summarize this information or provide a link to the information. (Tina Kapur)
The next annual report should include a link and reference to the User Manual for the NA-MIC Kit.(Will Schroeder)
What is the rational for choosing a particular method (tool) for solving a particular problem (DBP)? Why was a particular method (tool) chosen for development? Is there a listing of which tool might be helpful for which family of problems? Please provide more specific details to these questions as they have been asked previously by the Center Team. (Ross Whitaker)
A clinical project between Toronto and BWH still is recruitment phase in planning a DTI and genetic study of psychosis. What would be the genetic component? (Martha Shenton)
Drs. Martha Shenton (BWH) and James Kennedy (University of Toronto) are beginning a collaboration together based on mutual interests, although the specific goals have yet to be worked out. Specifically, Dr. Shenton is very much interested in developing further expertise in her laboratory in the area of genetics, particularly in area of white matter genes and their association with white matter fiber tract abnormalities evaluated using DTI in schizophrenia. Dr. Shenton has an instructor in Psychiatry at BWH who works in her laboratory who will be visiting Dr. Kennedy’s laboratory for a one week period in August of 2007, to be followed by several later visits, to learn state-of-the-art techniques used for evaluating white matter genes and their role in schizophrenia.
In parallel, Dr. Kennedy is very much interested in developing further expertise in his laboratory in the area of neuroimaging, particularly in both morphometry and DTI measures of white matter in schizophrenia, which he will correlate with genetic data involving white matter genes. Following up on this interest, Dr. Kennedy has a 4th year resident in psychiatry at the University of Toronto School of Medicine who works in his laboratory and who is visiting Dr. Shenton’s laboratory from July 1, 2007 to December 31, 2007, to learn state-of-the-art neuroimaging techniques including DTI and its application to understanding white matter pathology in schizophrenia. It is too early at this point to determine where this collaboration will go although it is clear that there is a tremendous amount of interest on both Dr. Shenton’s and Dr. Kennedy’s part, and the hope is that these early efforts will come to fruition in a grant that supports this collaborative endeavor.
The visualization tool allows the overlay of spherical, vector and ellipsoid data onto surfaces via versatile color maps. Is this extensible to other data, such a genetic or molecular data? (Steve Pieper)
The NA-MIC Kit is a set of compatible tools including utilities, libraries, and applications. At the application level, there are many promising areas of genetic or molecular research to which 3D Slicer has not been applied. 3D Slicer is extensible though, with current active projects and pending collaboration grant proposals to adapt and enhance the application to process microscopy data. For example, Drs. Bryan Smith and Mark Ellisman of UCSD are working on this topic through a supplement via the NCBC program. In addition Drs. Machiraju, Pieper, Aylward, and Davis of Ohio State, Isomics, and Kitware have jointly applied for a NA-MIC collaboration grant with the goal of implementing advanced image analysis algorithms that are well adapted to detecting cellular structures (currently in review). Dr. Gouaillard of CalTech is also collaborating with NA-MIC to adapt tools from the Center of Excellence in Genomic Science (CEGS) to work with their studies of the zebra fish embryogenesis. Beyond these specific examples, a wide range of research applications from surgery planning to astronomy have been enabled by the software. As the slicer3 platform matures, an even larger range of applications is anticipated. At the library and utility levels an even greater diversity of applications is possible as demonstrated by the range of applications using VTK and the applications developed on ITK.
Our approach to extending our software into new fields, such as the wider ranges of genetic or molecular images mentioned in the question, is to identify collaborators who need new image computing solutions of the type NA-MIC is providing. These collaborations often start through technical points of contact; programmers often research open source tools and begin 'tinkering' to see what can be re-used in a new application. If there is sufficient interest, these experiments can grow into collaboration in new fields. For example the collaboration with University of Iowa on Finite Element Meshing applies the software in a new direction that other NA-MIC developers had not been exploring.
