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Color display abnormal after gray scaling using opencv in Python
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I am trying to use Opencv in python to process digital pathology images. I convert the csv image into array and I want to convert the image to gray scale, here is my code:
start = time.time()
slide = openslide.open_slide("/Users/mihaoyang/Desktop/Pathology_Images/348980_case2_CD4.svs")
level_count = slide.level_count
print('level_count = ', level_count)
[column, row] = slide.dimensions
print('dimensions = ', column, row)
[column0, row0] = slide.level_dimensions[0]
[column1, row1] = slide.level_dimensions[1]
[column2, row2] = slide.level_dimensions[2]
print('dimensions[0] = ', [column0, row0])
print('dimensions[1] = ', [column1, row1])
print('dimensions[2] = ', [column2, row2])
slide_level_downsamples = slide.level_downsamples[2]
print(slide_level_downsamples)
slide_downsamples = slide.get_best_level_for_downsample(20.0)
print(slide_downsamples)
slide_normal = numpy.array(slide.read_region((12000, 15500), 0, (500, 500)))
slide_gray = numpy.array(slide.read_region((12000, 15500), 0, (500, 500)).convert('L'))
After I run the code, the following image was obtained
python numpy opencv image-processing
asked Jan 3 at 6:19
HAOYANG MIHAOYANG MI
557
add a comment |
I am trying to use Opencv in python to process digital pathology images. I convert the csv image into array and I want to convert the image to gray scale, here is my code:
start = time.time()
slide = openslide.open_slide("/Users/mihaoyang/Desktop/Pathology_Images/348980_case2_CD4.svs")
level_count = slide.level_count
print('level_count = ', level_count)
[column, row] = slide.dimensions
print('dimensions = ', column, row)
[column0, row0] = slide.level_dimensions[0]
[column1, row1] = slide.level_dimensions[1]
[column2, row2] = slide.level_dimensions[2]
print('dimensions[0] = ', [column0, row0])
print('dimensions[1] = ', [column1, row1])
print('dimensions[2] = ', [column2, row2])
slide_level_downsamples = slide.level_downsamples[2]
print(slide_level_downsamples)
slide_downsamples = slide.get_best_level_for_downsample(20.0)
print(slide_downsamples)
slide_normal = numpy.array(slide.read_region((12000, 15500), 0, (500, 500)))
slide_gray = numpy.array(slide.read_region((12000, 15500), 0, (500, 500)).convert('L'))
After I run the code, the following image was obtained
python numpy opencv image-processing
asked Jan 3 at 6:19
HAOYANG MIHAOYANG MI
557
2
What's the problem? And the code you show doesn't actually save an image as far as I can see. Nor does it contain the necessaryimportstatements so it can't be run.
– Mark Setchell
Jan 3 at 8:03
add a comment |
I am trying to use Opencv in python to process digital pathology images. I convert the csv image into array and I want to convert the image to gray scale, here is my code:
start = time.time()
slide = openslide.open_slide("/Users/mihaoyang/Desktop/Pathology_Images/348980_case2_CD4.svs")
level_count = slide.level_count
print('level_count = ', level_count)
[column, row] = slide.dimensions
print('dimensions = ', column, row)
[column0, row0] = slide.level_dimensions[0]
[column1, row1] = slide.level_dimensions[1]
[column2, row2] = slide.level_dimensions[2]
print('dimensions[0] = ', [column0, row0])
print('dimensions[1] = ', [column1, row1])
print('dimensions[2] = ', [column2, row2])
slide_level_downsamples = slide.level_downsamples[2]
print(slide_level_downsamples)
slide_downsamples = slide.get_best_level_for_downsample(20.0)
print(slide_downsamples)
slide_normal = numpy.array(slide.read_region((12000, 15500), 0, (500, 500)))
slide_gray = numpy.array(slide.read_region((12000, 15500), 0, (500, 500)).convert('L'))
After I run the code, the following image was obtained
python numpy opencv image-processing
asked Jan 3 at 6:19
HAOYANG MIHAOYANG MI
557
I am trying to use Opencv in python to process digital pathology images. I convert the csv image into array and I want to convert the image to gray scale, here is my code:
start = time.time()
slide = openslide.open_slide("/Users/mihaoyang/Desktop/Pathology_Images/348980_case2_CD4.svs")
level_count = slide.level_count
print('level_count = ', level_count)
[column, row] = slide.dimensions
print('dimensions = ', column, row)
[column0, row0] = slide.level_dimensions[0]
[column1, row1] = slide.level_dimensions[1]
[column2, row2] = slide.level_dimensions[2]
print('dimensions[0] = ', [column0, row0])
print('dimensions[1] = ', [column1, row1])
print('dimensions[2] = ', [column2, row2])
slide_level_downsamples = slide.level_downsamples[2]
print(slide_level_downsamples)
slide_downsamples = slide.get_best_level_for_downsample(20.0)
print(slide_downsamples)
slide_normal = numpy.array(slide.read_region((12000, 15500), 0, (500, 500)))
slide_gray = numpy.array(slide.read_region((12000, 15500), 0, (500, 500)).convert('L'))
After I run the code, the following image was obtained
python numpy opencv image-processing
python numpy opencv image-processing
asked Jan 3 at 6:19
HAOYANG MIHAOYANG MI
557
asked Jan 3 at 6:19
HAOYANG MIHAOYANG MI
557
asked Jan 3 at 6:19
HAOYANG MIHAOYANG MI
557
asked Jan 3 at 6:19
HAOYANG MIHAOYANG MI
557
asked Jan 3 at 6:19
HAOYANG MIHAOYANG MI
557
557
2
What's the problem? And the code you show doesn't actually save an image as far as I can see. Nor does it contain the necessaryimportstatements so it can't be run.
– Mark Setchell
Jan 3 at 8:03
add a comment |
2
What's the problem? And the code you show doesn't actually save an image as far as I can see. Nor does it contain the necessaryimportstatements so it can't be run.
– Mark Setchell
Jan 3 at 8:03
2
2
What's the problem? And the code you show doesn't actually save an image as far as I can see. Nor does it contain the necessary
import statements so it can't be run.– Mark Setchell
Jan 3 at 8:03
What's the problem? And the code you show doesn't actually save an image as far as I can see. Nor does it contain the necessary
import statements so it can't be run.– Mark Setchell
Jan 3 at 8:03
add a comment |
1 Answer
1
active
oldest
votes
Assuming you are using MatPlotLib to plot the image it looks like it is viridis colormap check them out here. If you want to change the colormap to gray scale pass gray into plt.imshow().
i.e.
plt.figure()
plt.imshow(slide_gray, 'gray')
plt.show()
If you're not using matplotlib then that will still be your problem so check out the image plotting library documentation for changing colormaps.
answered Jan 3 at 14:13
D.GriffithsD.Griffiths
7461317
add a comment |
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1 Answer
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active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
Assuming you are using MatPlotLib to plot the image it looks like it is viridis colormap check them out here. If you want to change the colormap to gray scale pass gray into plt.imshow().
i.e.
plt.figure()
plt.imshow(slide_gray, 'gray')
plt.show()
If you're not using matplotlib then that will still be your problem so check out the image plotting library documentation for changing colormaps.
answered Jan 3 at 14:13
D.GriffithsD.Griffiths
7461317
add a comment |
Assuming you are using MatPlotLib to plot the image it looks like it is viridis colormap check them out here. If you want to change the colormap to gray scale pass gray into plt.imshow().
i.e.
plt.figure()
plt.imshow(slide_gray, 'gray')
plt.show()
If you're not using matplotlib then that will still be your problem so check out the image plotting library documentation for changing colormaps.
answered Jan 3 at 14:13
D.GriffithsD.Griffiths
7461317
add a comment |
Assuming you are using MatPlotLib to plot the image it looks like it is viridis colormap check them out here. If you want to change the colormap to gray scale pass gray into plt.imshow().
i.e.
plt.figure()
plt.imshow(slide_gray, 'gray')
plt.show()
If you're not using matplotlib then that will still be your problem so check out the image plotting library documentation for changing colormaps.
answered Jan 3 at 14:13
D.GriffithsD.Griffiths
7461317
Assuming you are using MatPlotLib to plot the image it looks like it is viridis colormap check them out here. If you want to change the colormap to gray scale pass gray into plt.imshow().
i.e.
plt.figure()
plt.imshow(slide_gray, 'gray')
plt.show()
If you're not using matplotlib then that will still be your problem so check out the image plotting library documentation for changing colormaps.
answered Jan 3 at 14:13
D.GriffithsD.Griffiths
7461317
answered Jan 3 at 14:13
D.GriffithsD.Griffiths
7461317
answered Jan 3 at 14:13
D.GriffithsD.Griffiths
7461317
answered Jan 3 at 14:13
D.GriffithsD.Griffiths
7461317
7461317
add a comment |
add a comment |
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2
What's the problem? And the code you show doesn't actually save an image as far as I can see. Nor does it contain the necessary
importstatements so it can't be run.– Mark Setchell
Jan 3 at 8:03