Read in part of large histological (ndpi) file
I want to read in a very large histological image file (file size: 2.05 GB, *.ndpi file, pixel size: 57856 x 1.111e+05) and don’t have enough RAM.
I tried blockedImage and thought it would fit great but still, I am unable to get my data in highest resolution.
I tried:
% p,f are path and filename for the 2.05 GB *.ndpi file
A = blockedImage(strcat(p,f));
levelSizeInfo = table((1:length(A.Size))’, …
A.Size(:,1), …
A.Size(:,2), …
A.Size(:,1)./A.Size(:,2), …
‘VariableNames’,["Resolution Level" "Image Width" "Image Height" "Aspect Ratio"])
and obtained
levelSizeInfo =
9×4 table
Resolution Level Image Width Image Height Aspect Ratio
________________ ___________ ____________ ____________
1 57856 1.111e+05 0.52074
2 28928 55552 0.52074
3 14464 27776 0.52074
4 7232 13888 0.52074
5 3616 6944 0.52074
6 1808 3472 0.52074
7 904 1736 0.52074
8 407 1188 0.34259
9 203 594 0.34175
So I want to assess the resolution level 1 information and therefore tried to split it up in smaller patches:
bls = selectBlockLocations(A,"Levels",1,"BlockSize",[4096, 4096]);
bimds = blockedImageDatastore(A, "BlockLocationSet", bls);
However, I cannot assess these 4096 x 4096 blocks.
I tried to work with:
>> while hasdata(bimds)
[data, info] = read(bimds);
disp(info);
end
Error using images.blocked.TIFF/getIOBlock (line 139)
Out of memory.
But get the above error message. Is there any possibility that I read in my large image and split it up until my memory is sufficient and then assess the data? I don’t want to use lower resolution, since I am really interested in some specific histological information only reliable visible as highest resolution.
I would be also happy, when I would provide voxel coordinate start and end position and split it up manually such that it fits my RAM. I can do it in python but I would like to work with this dataset in Matlab as well.
Similar to this (which was not working either):
>> img = bigimage(strcat(p,f));
%Starting coordinates
coordStart = [250 250];
%Ending Coordinates
coordEnd = [750,750];
%Extract the region between the aforementioned coordinates
blk1 = getRegion(img,1,coordStart, coordEnd);
%Display the image
bigimageshow(bigimage(blk1))
Error using imread (line 440)
Unable to read TIFF file "SSES-1_MAX.ndpi". File is corrupt or image does not contain any readable strips.
Thanks in advance!I want to read in a very large histological image file (file size: 2.05 GB, *.ndpi file, pixel size: 57856 x 1.111e+05) and don’t have enough RAM.
I tried blockedImage and thought it would fit great but still, I am unable to get my data in highest resolution.
I tried:
% p,f are path and filename for the 2.05 GB *.ndpi file
A = blockedImage(strcat(p,f));
levelSizeInfo = table((1:length(A.Size))’, …
A.Size(:,1), …
A.Size(:,2), …
A.Size(:,1)./A.Size(:,2), …
‘VariableNames’,["Resolution Level" "Image Width" "Image Height" "Aspect Ratio"])
and obtained
levelSizeInfo =
9×4 table
Resolution Level Image Width Image Height Aspect Ratio
________________ ___________ ____________ ____________
1 57856 1.111e+05 0.52074
2 28928 55552 0.52074
3 14464 27776 0.52074
4 7232 13888 0.52074
5 3616 6944 0.52074
6 1808 3472 0.52074
7 904 1736 0.52074
8 407 1188 0.34259
9 203 594 0.34175
So I want to assess the resolution level 1 information and therefore tried to split it up in smaller patches:
bls = selectBlockLocations(A,"Levels",1,"BlockSize",[4096, 4096]);
bimds = blockedImageDatastore(A, "BlockLocationSet", bls);
However, I cannot assess these 4096 x 4096 blocks.
I tried to work with:
>> while hasdata(bimds)
[data, info] = read(bimds);
disp(info);
end
Error using images.blocked.TIFF/getIOBlock (line 139)
Out of memory.
But get the above error message. Is there any possibility that I read in my large image and split it up until my memory is sufficient and then assess the data? I don’t want to use lower resolution, since I am really interested in some specific histological information only reliable visible as highest resolution.
I would be also happy, when I would provide voxel coordinate start and end position and split it up manually such that it fits my RAM. I can do it in python but I would like to work with this dataset in Matlab as well.
Similar to this (which was not working either):
>> img = bigimage(strcat(p,f));
%Starting coordinates
coordStart = [250 250];
%Ending Coordinates
coordEnd = [750,750];
%Extract the region between the aforementioned coordinates
blk1 = getRegion(img,1,coordStart, coordEnd);
%Display the image
bigimageshow(bigimage(blk1))
Error using imread (line 440)
Unable to read TIFF file "SSES-1_MAX.ndpi". File is corrupt or image does not contain any readable strips.
Thanks in advance! I want to read in a very large histological image file (file size: 2.05 GB, *.ndpi file, pixel size: 57856 x 1.111e+05) and don’t have enough RAM.
I tried blockedImage and thought it would fit great but still, I am unable to get my data in highest resolution.
I tried:
% p,f are path and filename for the 2.05 GB *.ndpi file
A = blockedImage(strcat(p,f));
levelSizeInfo = table((1:length(A.Size))’, …
A.Size(:,1), …
A.Size(:,2), …
A.Size(:,1)./A.Size(:,2), …
‘VariableNames’,["Resolution Level" "Image Width" "Image Height" "Aspect Ratio"])
and obtained
levelSizeInfo =
9×4 table
Resolution Level Image Width Image Height Aspect Ratio
________________ ___________ ____________ ____________
1 57856 1.111e+05 0.52074
2 28928 55552 0.52074
3 14464 27776 0.52074
4 7232 13888 0.52074
5 3616 6944 0.52074
6 1808 3472 0.52074
7 904 1736 0.52074
8 407 1188 0.34259
9 203 594 0.34175
So I want to assess the resolution level 1 information and therefore tried to split it up in smaller patches:
bls = selectBlockLocations(A,"Levels",1,"BlockSize",[4096, 4096]);
bimds = blockedImageDatastore(A, "BlockLocationSet", bls);
However, I cannot assess these 4096 x 4096 blocks.
I tried to work with:
>> while hasdata(bimds)
[data, info] = read(bimds);
disp(info);
end
Error using images.blocked.TIFF/getIOBlock (line 139)
Out of memory.
But get the above error message. Is there any possibility that I read in my large image and split it up until my memory is sufficient and then assess the data? I don’t want to use lower resolution, since I am really interested in some specific histological information only reliable visible as highest resolution.
I would be also happy, when I would provide voxel coordinate start and end position and split it up manually such that it fits my RAM. I can do it in python but I would like to work with this dataset in Matlab as well.
Similar to this (which was not working either):
>> img = bigimage(strcat(p,f));
%Starting coordinates
coordStart = [250 250];
%Ending Coordinates
coordEnd = [750,750];
%Extract the region between the aforementioned coordinates
blk1 = getRegion(img,1,coordStart, coordEnd);
%Display the image
bigimageshow(bigimage(blk1))
Error using imread (line 440)
Unable to read TIFF file "SSES-1_MAX.ndpi". File is corrupt or image does not contain any readable strips.
Thanks in advance! histological data, ndpi, blockedimage MATLAB Answers — New Questions
