bigimageDatastore

Create a bigimage using a modified version of image "tumor_091.tif" from the CAMELYON16 data set. The original image is a training image of a lymph node containing tumor tissue. The original image has eight resolution levels, and the finest level has resolution 53760-by-61440. The modified image has only three coarse resolution levels. The spatial referencing of the modified image has been adjusted to enforce a consistent aspect ratio and to register features at each level.

bim = bigimage('tumor_091R.tif');

Display the default block size of the bigimage at each resolution level. The block size is a 2-element vector of the form [numrows, numcols].

t = table((1:3)',bim.BlockSize,'VariableNames',["Level" "Block Size"]);
disp(t)

    Level     Block Size 
    _____    ____________

      1      1024    1024
      2      1024    1024
      3      1024    1024

Display the bigimage by using the bigimageshow function.

bigimageshow(bim);

Create a bigimageDatastore at resolution level 1. Specify a nondefault block size. Set the datastore to read four blocks at a time.

bimds = bigimageDatastore(bim,2,'BlockSize',[512 512],'ReadSize',4)

bimds = 
  bigimageDatastore with properties:

            ReadSize: 4
          BorderSize: [0 0]
           PadMethod: 0
              Images: [1×1 bigimage]
              Levels: 2
           BlockSize: [512 512]
        BlockOffsets: [512 512]
    IncompleteBlocks: 'same'
    BlockLocationSet: [1×1 blockLocationSet]

Read one batch of data from the datastore. Notice that the third block is a partial edge block and has a smaller size than interior blocks. Display the returned image patches as a montage. The montage displays the third block with a thicker border because the width of the block is smaller than the width of the complete blocks.

blocks = read(bimds)

blocks=4×1 cell array
    {512×512×3 uint8}
    {512×512×3 uint8}
    {512×316×3 uint8}
    {512×512×3 uint8}

montage(blocks,'Size',[1 bimds.ReadSize],'BorderSize',5,'BackgroundColor','k');

Read the next batch of data from the datastore and display the returned image patches as a montage. The montage displays partial blocks with a thicker border because the dimensions of the blocks are smaller than the dimensions of the full block.

blocks = read(bimds)

blocks=4×1 cell array
    {512×512×3 uint8}
    {512×316×3 uint8}
    {226×512×3 uint8}
    {226×512×3 uint8}

montage(blocks,'Size',[1 bimds.ReadSize],'BorderSize',5,'BackgroundColor','k');

Read the last batch of data from the datastore. The read operation returns a partial batch that contains the only remaining patch. Display the patch.

blocks = read(bimds)

blocks = 1×1 cell array
    {226×316×3 uint8}

montage(blocks,'Size',[1 bimds.ReadSize],'BorderSize',5,'BackgroundColor','k');

Create a bigimage using a modified version of image "tumor_091.tif" from the CAMELYON16 data set. The original image is a training image of a lymph node containing tumor tissue. The original image has eight resolution levels, and the finest level has resolution 53760-by-61440. The modified image has only three coarse resolution levels. The spatial referencing of the modified image has been adjusted to enforce a consistent aspect ratio and to register features at each level.

bim = bigimage("tumor_091R.tif");

Display the bigimage by using the bigimageshow function.

h = bigimageshow(bim);

Create a mask at the coarsest resolution level, retaining the original spatial referencing information.

clevel = bim.CoarsestResolutionLevel;
imcoarse = getFullLevel(bim,clevel);
stainMask = ~imbinarize(im2gray(imcoarse));
bmask = bigimage(stainMask,"SpatialReferencing",bim.SpatialReferencing(clevel));

Specify the location of blocks to read from the bigimage by using the selectBlockLocations function. Set the block size as 256-by-256 pixels. Select blocks that are at least 75% within the ROI defined by the mask by specifying the "InclusionThreshold" name-value pair argument. By default, selectBlockLocations selects blocks from the finest resolution level of the big image.

t = 0.75;
blockSize = [256 256];
blockSet = selectBlockLocations(bim,"BlockSize",blockSize, ...
    "Masks",bmask,"InclusionThreshold",t);

Create a bigimageDatastore that reads four blocks at a time from the locations specified by the blockLocationSet.

bimds = bigimageDatastore(bim,"BlockLocationSet",blockSet,"ReadSize",4);

To preview which patches are read by the datastore, display the mask over the original bigimage using the same block size and inclusion threshold. The overlay highlights in green the patches that are at least 75% within the ROI defined by the mask.

showmask(h,bmask,"BlockSize",blockSize,"InclusionThreshold",t)

Read the first batch of data from the datastore and display the returned image patches as a montage. The content of these patches matches the green blocks of the overlay.

blocks = read(bimds);
montage(blocks,"Size",[1 bimds.ReadSize],"BorderSize",5,"BackgroundColor","k");

Create a bigimage using a modified version of image "tumor_091.tif" from the CAMELYON16 data set. The original image is a training image of a lymph node containing tumor tissue. The original image has eight resolution levels, and the finest level has resolution 53760-by-61440. The modified image has only three coarse resolution levels. The spatial referencing of the modified image has been adjusted to enforce a consistent aspect ratio and to register features at each level.

bim = bigimage('tumor_091R.tif');

Display the entire bigimage at the finest resolution level.

bshow = bigimageshow(bim);

Specify four [x y] block locations from the finest level. The first two blocks overlap in the vertical direction. The second two blocks are adjacent horizontally.

xyLocations = [ ...
    2800 1300; ...
    2800 1400; ...
    1500 2400; ...
    1800 2400];
blockSize = [300,300];

All blocks are from the same image. Specify the image number as 1 for all blocks.

imageNumber = [1 1 1 1]';

Create a blockLocationSet object that stores block locations.

locationSet = blockLocationSet(imageNumber,xyLocations,blockSize);

Create a bigimageDatastore object that reads blocks from big image bim at locations specified by the blockLocationSet object.

bimds = bigimageDatastore(bim,'BlockLocationSet',locationSet);

Read two blocks at a time from the datastore and display them in a montage.

bimds.ReadSize = 2;
while hasdata(bimds)
    figure
    blocks = read(bimds);
    montage(blocks,'BorderSize',5,'BackgroundColor','b');
end