Difference between revisions of "Project Week 25/Multimodal:"
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==Key Investigators== | ==Key Investigators== | ||
<!-- Key Investigator bullet points --> | <!-- Key Investigator bullet points --> | ||
− | * | + | *Guido Gerig (NYU Tandon School of Engineering) |
− | * | + | *Sungmin Hong (NYU Tandon School of Engineering) |
− | |||
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! style="text-align: left; width:27%" | Progress and Next Steps | ! style="text-align: left; width:27%" | Progress and Next Steps | ||
|- style="vertical-align:top;" | |- style="vertical-align:top;" | ||
− | |<!-- Objective bullet points --> | + | | |
+ | <!-- Objective bullet points --> | ||
− | + | 3D/4D Ophthalmology Image Anaylsis Framework | |
− | + | * Read 4D hyperspectral data | |
+ | * Viewer and interactor for 3D hi-res image data and 4D hyperspectral data | ||
+ | * Co-registration between 3D hi-res data and 4D hyperspectral data | ||
+ | * Cell segmentation in 3D hi-res data | ||
+ | * Statistics of cells (possibly location, size, distribution) | ||
+ | * Plot of spectra of selected cells or a region-of-interest | ||
+ | | | ||
− | | | + | <!-- Approach and Plan bullet points --> |
+ | * Review existing modules in 3D Slicer | ||
+ | ** Review existing modules for 4D data viewer, such as, multi-volume viewer extension | ||
+ | ** Try existing segmentation modules in Slicer to see if they can work on SIM data | ||
+ | ** Review existing modules for cell statistics after segmentation | ||
+ | |||
+ | * Implementation/Integration | ||
+ | ** Implement/integrate 4D hyperspectral data viewer to show image and spectral information. | ||
+ | ** Integrate registration functionality for co-registration between 3D hi-res data and 4D hyperspectral data at image level | ||
+ | ** Integrate user-initialized level set segmentation for cell segmentation or EM segmentation module | ||
+ | ** Implement a viewer and an interactor for cell statistics | ||
+ | |||
+ | * User Manual | ||
+ | ** Create an user manual to comprehend a overview of an extension | ||
+ | ** Guide users to different extensions in a algorithmic flow chart if there are any desired functions (registration, segmentation, or etc.) which are already implemented in existing modules. | ||
+ | |||
+ | | | ||
+ | <!-- Progress and Next steps bullet points (fill out at the end of project week --> | ||
+ | * Hyperspectral Analysis | ||
+ | ** Implemented a module to convert 4D LSM data to a series of 3D data compatible to MultiVolume Explorer | ||
+ | ** With a converted series of 3D data, MultiVolume explorer offered a basic analysis tool for hyperspectral data. | ||
+ | ** Label statistics or segmentation need to be added in the future | ||
+ | |||
+ | * Registration | ||
+ | ** Basic registration algorithms in Slicer worked well on linear registration between 3D SIM and a cropped and dimension reduced 4D LSM data. | ||
+ | ** Detecting corresponding regions of 3D SIM in 4D LSM data needs to be developed in the future. | ||
+ | |||
+ | * Segmentation | ||
+ | ** Watershed segmentation on 3D hi-res image data (WASP) was not successful. | ||
+ | ** Editor/Segmentation Editor worked good on slice-by-slice segmentation | ||
+ | ** Will investigate more on 3D segmentation capability of Slicer with possible collaboration with other groups. | ||
− | |||
− | + | |} | |
− | + | ==Illustrations== | |
==Background and References== | ==Background and References== | ||
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --> | <!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --> |
Revision as of 14:51, 12 June 2017
Home < Project Week 25 < Multimodal:
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Key Investigators
- Guido Gerig (NYU Tandon School of Engineering)
- Sungmin Hong (NYU Tandon School of Engineering)
Project Description
Objective | Approach and Plan | Progress and Next Steps |
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3D/4D Ophthalmology Image Anaylsis Framework
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