Project Week 25/Multimodal:

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Key Investigators

• Guido Gerig (NYU Tandon School of Engineering, USA)
• Sungmin Hong (NYU Tandon School of Engineering, USA)

Project Description

Project details can downloaded here as pptx or [File:File:Gerig-Slicer-6-26-2017-final.pdf pdf]

Objective	Approach and Plan	Progress and Next Steps
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	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.	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