Project Week 25/Multimodal: - Revision history

Gerig at 10:29, 30 June 2017

2017-06-30T10:29:15Z

Gerig at 10:26, 30 June 2017

2017-06-30T10:26:10Z

Gerig at 09:24, 30 June 2017

2017-06-30T09:24:06Z

Gerig at 08:57, 30 June 2017

2017-06-30T08:57:44Z

Jfishbaugh at 08:55, 30 June 2017

2017-06-30T08:55:44Z

Jfishbaugh at 08:55, 30 June 2017

2017-06-30T08:55:05Z

Jfishbaugh at 08:54, 30 June 2017

2017-06-30T08:54:32Z

Jfishbaugh: /* Project Description */

2017-06-30T08:52:07Z

Project Description

Jfishbaugh at 08:49, 30 June 2017

2017-06-30T08:49:52Z

Jfishbaugh: /* Project Description */

2017-06-30T08:49:15Z

Project Description

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 <!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data -->
-[1] Thomas Ach, Sungmin Hong, Rainer Heintzmann, Jost Hillenkamp, Kenneth R. Sloan, Neel Dey, Guido Gerig, R. Theodore Smith, Christine A. Curcio, Katharina Bermond, High-resolution and hyperspectral imaging of autofluorescent retinal pigment epithelium (RPE) granules, ARVO 2017 Annual Meeting Abstracts, No.  3382, [http://www.arvo.org/webs/am2017/sectionpdf/RC/Session%20363%20Macular%20degeneration-cell%20biology.pdf abstract]
+[1] Thomas Ach, Sungmin Hong, Rainer Heintzmann, Jost Hillenkamp, Kenneth R. Sloan, Neel Dey, Guido Gerig, R. Theodore Smith, Christine A. Curcio, Katharina Bermond, High-resolution and hyperspectral imaging of autofluorescent retinal pigment epithelium (RPE) granules, ARVO 2017 Annual Meeting Abstracts, No.  3382, [http://www.arvo.org/webs/am2017/sectionpdf/RC/Session%20363%20Macular%20degeneration-cell%20biology.pdf Abstract]
-[2] Tong Y, Ben Ami T, Hong S, Heintzmann R, Gerig G, Ablonczy Z, Curcio CA, Ach T, Smith RT., HYPERSPECTRAL AUTOFLUORESCENCE IMAGING OF DRUSEN AND RETINAL PIGMENT EPITHELIUM IN DONOR EYES WITH AGE-RELATED MACULAR DEGENERATION, Retina. 2016 Dec;36 Suppl 1:S127-S136. doi: 10.1097/IAE.0000000000001325., PMID: 28005671
+[2] Tong Y, Ben Ami T, Hong S, Heintzmann R, Gerig G, Ablonczy Z, Curcio CA, Ach T, Smith RT., HYPERSPECTRAL AUTOFLUORESCENCE IMAGING OF DRUSEN AND RETINAL PIGMENT EPITHELIUM IN DONOR EYES WITH AGE-RELATED MACULAR DEGENERATION, Retina. 2016 Dec;36 Suppl 1:S127-S136, [http://journals.lww.com/retinajournal/Citation/2016/12001/HYPERSPECTRAL_AUTOFLUORESCENCE_IMAGING_OF_DRUSEN.14.aspx Paper]

← Older revision		Revision as of 10:26, 30 June 2017
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	==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 -->
		+
		+	[1] Thomas Ach, Sungmin Hong, Rainer Heintzmann, Jost Hillenkamp, Kenneth R. Sloan, Neel Dey, Guido Gerig, R. Theodore Smith, Christine A. Curcio, Katharina Bermond, High-resolution and hyperspectral imaging of autofluorescent retinal pigment epithelium (RPE) granules, ARVO 2017 Annual Meeting Abstracts, No. 3382, [http://www.arvo.org/webs/am2017/sectionpdf/RC/Session%20363%20Macular%20degeneration-cell%20biology.pdf abstract]
		+
		+	[2] Tong Y, Ben Ami T, Hong S, Heintzmann R, Gerig G, Ablonczy Z, Curcio CA, Ach T, Smith RT., HYPERSPECTRAL AUTOFLUORESCENCE IMAGING OF DRUSEN AND RETINAL PIGMENT EPITHELIUM IN DONOR EYES WITH AGE-RELATED MACULAR DEGENERATION, Retina. 2016 Dec;36 Suppl 1:S127-S136. doi: 10.1097/IAE.0000000000001325., PMID: 28005671

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 ** 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
+** Explore most recent "Segment Editor" features for cell and organelle segmentation
 * User Manual
 ** Create an user manual to comprehend a overview of an extension
+|
 <!-- Progress and Next steps bullet points (fill out at the end of project week -->
-* Hyperspectral Analysis
+* Manual
-** Implemented a module to convert 4D LSM data to a series of 3D data compatible to MultiVolume Explorer
+** [https://na-mic.org/w/images/a/af/Tutorial_HOA.pdf Slicer tutorial] explaining multi-volume conversion and 3D/4D registration.
 * Registration
-** Basic registration algorithms in Slicer worked well on linear registration between 3D SIM and a cropped and dimension reduced 4D LSM data.
+** '''Basic registration algorithms in Slicer worked well for linear registration''' between 3D SIM and cropped and dimension reduced 4D LSM data.
-** Detecting corresponding regions of 3D SIM in 4D LSM data needs to be developed in the future.
+** Automatic detection of corresponding subregions between hires 3D SIM and low-res 4D LSM data may be implemented via autocorrelation.
 * Segmentation
-** Watershed segmentation on 3D hi-res image data (WASP) was not successful.
+** '''GrowCut segmentation worked well for 3D segmentation''' of organelles of different contrast, e.g. dark Lipofuscin and bright Melanolipofuscin as required by clinical researchers.
-** Editor/Segmentation Editor worked good on slice-by-slice segmentation
+** Cell segmentation/outlining and combination with organelle segmentation can be solved with the Segment Editor features.
-** Will investigate more on 3D segmentation capability of Slicer with possible collaboration with other groups.
 |}

@@ Line 20: / Line 20: @@
 <!-- Objective bullet points -->
-D/4D Ophthalmology Image Anaylsis Framework
+D/4D Ophthalmology Image Anaylsis Framework: Continuation of initial January 2017 project by Sungmin Hong:
 * Read 4D hyperspectral data
 * Viewer and interactor for 3D hi-res image data and 4D hyperspectral data

@@ Line 8: / Line 8: @@
 ==Project Description==
+* '''Project details can downloaded here as [http://research.engineering.nyu.edu/~fishbaugh/docs/Gerig-Slicer-6-26-2017-final.pptx pptx] or [https://na-mic.org/w/images/a/ae/Gerig-Slicer-6-26-2017-final.pdf pdf].'''
-<!-- Download bullet points -->
+* '''Download a [https://na-mic.org/w/images/a/af/Tutorial_HOA.pdf Slicer tutorial].'''

@@ Line 9: / Line 9: @@
 ==Project Description==
 '''*Project details can downloaded here as [http://research.engineering.nyu.edu/~fishbaugh/docs/Gerig-Slicer-6-26-2017-final.pptx pptx] or [https://na-mic.org/w/images/a/ae/Gerig-Slicer-6-26-2017-final.pdf pdf].'''
 '''*Download a [https://na-mic.org/w/images/a/af/Tutorial_HOA.pdf Slicer tutorial].'''

@@ Line 8: / Line 8: @@
 ==Project Description==
-Project details can downloaded here as [http://research.engineering.nyu.edu/~fishbaugh/docs/Gerig-Slicer-6-26-2017-final.pptx pptx] or [File:File:Gerig-Slicer-6-26-2017-final.pdf pdf]
+Project details can downloaded here as [http://research.engineering.nyu.edu/~fishbaugh/docs/Gerig-Slicer-6-26-2017-final.pptx pptx] or [File:File:Gerig-Slicer-6-26-2017-final.pdf | pdf]
 {| class="wikitable"