Mixing
EBImage cell segmentation, segmentation polygon saved to a Spatial Polygons
So I'm trying to connect EBImage output into 'sp' package to create a custom shape file (or SpatialPolygonDataFrame object).
Using the demo example from EBImage for cell segmentation, I am trying to output the polygonal segmentation into a 'SpatialPolygonDataFrame'.
The tricky part is that EBImage creates the polygon for me and stores into a large array.
How can I use this polygonal information/segmentation and create a 'SpatialPolygonDataFrame' using this example data?
The EBImage segmentation has a 510X510 RGB array for 4 images. The segmentation creates the desired polygonal boundary. Is it possible to use this polygonal boundary as a shape file for spatial analysis in the package 'sp' ?
nuc = readImage(system.file('images', 'nuclei.tif',
package='EBImage'))
cel = readImage(system.file('images', 'cells.tif',
package='EBImage'))
cells = rgbImage(green=1.5*cel, blue=nuc)
display(cells, all = TRUE)
nmask = thresh(nuc, w=10, h=10, offset=0.05)
nmask = opening(nmask, makeBrush(5, shape='disc'))
nmask = fillHull(nmask)
nmask = bwlabel(nmask)
display(nmask, all=TRUE)
ctmask = opening(cel>0.1, makeBrush(5, shape='disc'))
cmask = propagate(cel, seeds=nmask, mask=ctmask)
display(ctmask, all=TRUE)
segmented = paintObjects(cmask, cells, col='#ff00ff')
segmented = paintObjects(nmask, segmented, col='#ffff00')
display(segmented, all=TRUE)
> segmented
Image
colorMode : Color
storage.mode : double
dim : 510 510 3 4
frames.total : 12
frames.render: 4
imageData(object)[1:5,1:6,1,1]
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0 0 0 1 0 0
[2,] 0 0 0 1 0 0
[3,] 0 0 0 0 1 0
[4,] 0 0 0 0 0 1
[5,] 0 0 0 0 0 1
dim(imageData(segmented))
510 510 3 4
image-processing spatial sp
asked Nov 19 '18 at 23:41
sophie-germainsophie-germain
2372418
add a comment |
So I'm trying to connect EBImage output into 'sp' package to create a custom shape file (or SpatialPolygonDataFrame object).
Using the demo example from EBImage for cell segmentation, I am trying to output the polygonal segmentation into a 'SpatialPolygonDataFrame'.
The tricky part is that EBImage creates the polygon for me and stores into a large array.
How can I use this polygonal information/segmentation and create a 'SpatialPolygonDataFrame' using this example data?
The EBImage segmentation has a 510X510 RGB array for 4 images. The segmentation creates the desired polygonal boundary. Is it possible to use this polygonal boundary as a shape file for spatial analysis in the package 'sp' ?
nuc = readImage(system.file('images', 'nuclei.tif',
package='EBImage'))
cel = readImage(system.file('images', 'cells.tif',
package='EBImage'))
cells = rgbImage(green=1.5*cel, blue=nuc)
display(cells, all = TRUE)
nmask = thresh(nuc, w=10, h=10, offset=0.05)
nmask = opening(nmask, makeBrush(5, shape='disc'))
nmask = fillHull(nmask)
nmask = bwlabel(nmask)
display(nmask, all=TRUE)
ctmask = opening(cel>0.1, makeBrush(5, shape='disc'))
cmask = propagate(cel, seeds=nmask, mask=ctmask)
display(ctmask, all=TRUE)
segmented = paintObjects(cmask, cells, col='#ff00ff')
segmented = paintObjects(nmask, segmented, col='#ffff00')
display(segmented, all=TRUE)
> segmented
Image
colorMode : Color
storage.mode : double
dim : 510 510 3 4
frames.total : 12
frames.render: 4
imageData(object)[1:5,1:6,1,1]
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0 0 0 1 0 0
[2,] 0 0 0 1 0 0
[3,] 0 0 0 0 1 0
[4,] 0 0 0 0 0 1
[5,] 0 0 0 0 0 1
dim(imageData(segmented))
510 510 3 4
image-processing spatial sp
asked Nov 19 '18 at 23:41
sophie-germainsophie-germain
2372418
add a comment |
So I'm trying to connect EBImage output into 'sp' package to create a custom shape file (or SpatialPolygonDataFrame object).
Using the demo example from EBImage for cell segmentation, I am trying to output the polygonal segmentation into a 'SpatialPolygonDataFrame'.
The tricky part is that EBImage creates the polygon for me and stores into a large array.
How can I use this polygonal information/segmentation and create a 'SpatialPolygonDataFrame' using this example data?
The EBImage segmentation has a 510X510 RGB array for 4 images. The segmentation creates the desired polygonal boundary. Is it possible to use this polygonal boundary as a shape file for spatial analysis in the package 'sp' ?
nuc = readImage(system.file('images', 'nuclei.tif',
package='EBImage'))
cel = readImage(system.file('images', 'cells.tif',
package='EBImage'))
cells = rgbImage(green=1.5*cel, blue=nuc)
display(cells, all = TRUE)
nmask = thresh(nuc, w=10, h=10, offset=0.05)
nmask = opening(nmask, makeBrush(5, shape='disc'))
nmask = fillHull(nmask)
nmask = bwlabel(nmask)
display(nmask, all=TRUE)
ctmask = opening(cel>0.1, makeBrush(5, shape='disc'))
cmask = propagate(cel, seeds=nmask, mask=ctmask)
display(ctmask, all=TRUE)
segmented = paintObjects(cmask, cells, col='#ff00ff')
segmented = paintObjects(nmask, segmented, col='#ffff00')
display(segmented, all=TRUE)
> segmented
Image
colorMode : Color
storage.mode : double
dim : 510 510 3 4
frames.total : 12
frames.render: 4
imageData(object)[1:5,1:6,1,1]
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0 0 0 1 0 0
[2,] 0 0 0 1 0 0
[3,] 0 0 0 0 1 0
[4,] 0 0 0 0 0 1
[5,] 0 0 0 0 0 1
dim(imageData(segmented))
510 510 3 4
image-processing spatial sp
asked Nov 19 '18 at 23:41
sophie-germainsophie-germain
2372418
So I'm trying to connect EBImage output into 'sp' package to create a custom shape file (or SpatialPolygonDataFrame object).
Using the demo example from EBImage for cell segmentation, I am trying to output the polygonal segmentation into a 'SpatialPolygonDataFrame'.
The tricky part is that EBImage creates the polygon for me and stores into a large array.
How can I use this polygonal information/segmentation and create a 'SpatialPolygonDataFrame' using this example data?
The EBImage segmentation has a 510X510 RGB array for 4 images. The segmentation creates the desired polygonal boundary. Is it possible to use this polygonal boundary as a shape file for spatial analysis in the package 'sp' ?
nuc = readImage(system.file('images', 'nuclei.tif',
package='EBImage'))
cel = readImage(system.file('images', 'cells.tif',
package='EBImage'))
cells = rgbImage(green=1.5*cel, blue=nuc)
display(cells, all = TRUE)
nmask = thresh(nuc, w=10, h=10, offset=0.05)
nmask = opening(nmask, makeBrush(5, shape='disc'))
nmask = fillHull(nmask)
nmask = bwlabel(nmask)
display(nmask, all=TRUE)
ctmask = opening(cel>0.1, makeBrush(5, shape='disc'))
cmask = propagate(cel, seeds=nmask, mask=ctmask)
display(ctmask, all=TRUE)
segmented = paintObjects(cmask, cells, col='#ff00ff')
segmented = paintObjects(nmask, segmented, col='#ffff00')
display(segmented, all=TRUE)
> segmented
Image
colorMode : Color
storage.mode : double
dim : 510 510 3 4
frames.total : 12
frames.render: 4
imageData(object)[1:5,1:6,1,1]
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0 0 0 1 0 0
[2,] 0 0 0 1 0 0
[3,] 0 0 0 0 1 0
[4,] 0 0 0 0 0 1
[5,] 0 0 0 0 0 1
dim(imageData(segmented))
510 510 3 4
image-processing spatial sp
image-processing spatial sp
asked Nov 19 '18 at 23:41
sophie-germainsophie-germain
2372418
asked Nov 19 '18 at 23:41
sophie-germainsophie-germain
2372418
asked Nov 19 '18 at 23:41
sophie-germainsophie-germain
2372418
asked Nov 19 '18 at 23:41
sophie-germainsophie-germain
2372418
asked Nov 19 '18 at 23:41
sophie-germainsophie-germain
2372418
2372418
add a comment |
add a comment |
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