2009 Winter Project Week Tumor Microenvironment - Revision history

Singhsh at 17:36, 9 January 2009

2009-01-09T17:36:39Z

2009-01-09T17:35:38Z

2009-01-09T17:17:07Z

2009-01-05T19:04:34Z

2009-01-05T19:03:21Z

2009-01-05T18:14:46Z

2009-01-05T17:55:40Z

Key Investigators

2009-01-05T17:27:58Z

Key Investigators

2009-01-05T17:25:29Z

2009-01-05T17:11:06Z

Key Investigators

@@ Line 40: / Line 40: @@
 We wanted to investigate the use of Slicer3 for building a microscopy pipeline and integrate some of the modules of our existing pipeline into Slicer. To start off we used the execution model to load our segmentation algorithm through slicer and  started working on building a loadable module for slicer.
-We got Grid Wizard running and set up for our pipeline (need to resolve resource manager issue)
+We got Grid Wizard (Marco) running and set up for our pipeline (need to resolve resource manager issue)
 We had discussions (Wendy/Curtis) on annotation capabilities of Slicer3 that will be useful for the tumor microscopy datasets

← Older revision		Revision as of 17:35, 9 January 2009
Line 42:		Line 42:
	We got Grid Wizard running and set up for our pipeline (need to resolve resource manager issue)		We got Grid Wizard running and set up for our pipeline (need to resolve resource manager issue)

		+	We had discussions (Wendy/Curtis) on annotation capabilities of Slicer3 that will be useful for the tumor microscopy datasets

	</div>		</div>

← Older revision		Revision as of 17:17, 9 January 2009
Line 38:		Line 38:
	<h1>Progress</h1>		<h1>Progress</h1>

−	~~Updated every day~~ of ~~Project Week~~.	+	We wanted to investigate the use of Slicer3 for building a microscopy pipeline and integrate some of the modules of our existing pipeline into Slicer. To start off we used the execution model to load our segmentation algorithm through slicer and started working on building a loadable module for slicer.
		+
		+	We got Grid Wizard running and set up for our pipeline (need to resolve resource manager issue)

@@ Line 2: / Line 2: @@
 |[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week]] ]]
 |[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
-|[[Image:snap3.jpg|thumb|320px|[http://www.nature.com.proxy.lib.ohio-state.edu/nrc/journal/v7/n9/fig_tab/nrc2193_F1.html#figure-title Fig 2.]]]
+|[[Image:snap3.jpg|thumb|320px|[http://www.nature.com/nrc/journal/v7/n9/fig_tab/nrc2193_F1.html#figure-title Fig 2.]]]
 |}

@@ Line 2: / Line 2: @@
 |[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week]] ]]
 |[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
-|[[Image:snap3.jpg|thumb|320px|]]
+|[[Image:snap3.jpg|thumb|320px|[http://www.nature.com.proxy.lib.ohio-state.edu/nrc/journal/v7/n9/fig_tab/nrc2193_F1.html#figure-title Fig 2.]]]
 |}

@@ Line 10: / Line 10: @@
 ===Key Investigators===
-* The Ohio State University: Shantanu Singh, Raghu Machiraju
+* The Ohio State University: Shantanu Singh, Raghu Machiraju, Gustavo Leone, Michael Ostrowksi
 * GE Global Research: Jens Rittscher
 * BWH: Michael Halle, Steve Pieper, Wendy Plesniak

@@ Line 29: / Line 29: @@
 Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
-Begin with level set methods of [Mosaliganti 2008] (middle image). Then the tessellation based method of the same authors, time permitting.  Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
+Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting.  Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
 Also, explore  labeling capabilities of Slicer3.

@@ Line 1: / Line 1: @@
 {|
 |[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
-|[[Image:Tme_snapshot2.jpg|thumb|320px|]]
+|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
 |[[Image:snap3.jpg|thumb|320px|]]
 |}