View source for Project Week 25/Multimodal:

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==Key Investigators==
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*Guido Gerig (NYU Tandon School of Engineering)
*Sungmin Hong (NYU Tandon School of Engineering)


==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" |   Objective
! style="text-align: left; width:27%" |   Approach and Plan
! style="text-align: left; width:27%" |   Progress and Next Steps
|- style="vertical-align:top;"
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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
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<!-- 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.

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<!-- 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.



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==Illustrations==

==Background and References==
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