mergeBlockLocationSets

Create a blocked image.

bim = blockedImage("tumor_091R.tif");
blockSize = [128 128];

Create a mask at the coarsest level. The mask corresponds to regions of the image that contain tissue.

clevel = bim.NumLevels;
bmask = apply(bim,@(b)~imbinarize(im2gray(b.Data)),Level=clevel);

Display all regions with tissue. Specify a region as having tissue when at least 20% of pixels are true in the stained region, as defined by the mask.

threshTissue = 0.2;
figure
h1 = bigimageshow(bim);
showmask(h1,bmask,BlockSize=blockSize,InclusionThreshold=threshTissue)
title("Highlighted Tissue Mask")

The tissue regions occupy a large portion of the image. When selecting tissue blocks, reduce the size of the data set by adding a gap between sampled blocks. The returned blockLocationSet object contains 184 tissue blocks.

undersampleFactor = 1.5;
bls1 = selectBlockLocations(bim,BlockSize=blockSize,Masks=bmask, ...
    InclusionThreshold=threshTissue,BlockOffsets=blockSize*undersampleFactor)

bls1 = 
  blockLocationSet with properties:

    ImageNumber: [184×1 double]
    BlockOrigin: [184×3 double]
      BlockSize: [128 128 3]
         Levels: 1

Display the relatively homogeneous regions. Define a homogeneous region as a region in which at least 90% of pixels are true in the stained region, as defined by the mask.

threshHomogeneous = 0.9;
h2 = bigimageshow(bim);
showmask(h2,bmask,BlockSize=blockSize,InclusionThreshold=threshHomogeneous)
title("Highlighted " + threshHomogeneous*100 + "% Uniform Regions")

The homogeneous regions occupy a much smaller portion of the image. To select a balanced number of blocks, oversample the homogeneous blocks. The returned blockLocationSet object contains 166 homogeneous blocks.

oversampleFactor = 2;
bls2 = selectBlockLocations(bim,BlockSize=blockSize,Levels=1,Masks=bmask, ...
    InclusionThreshold=threshHomogeneous,BlockOffsets=blockSize/oversampleFactor)

bls2 = 
  blockLocationSet with properties:

    ImageNumber: [166×1 double]
    BlockOrigin: [166×3 double]
      BlockSize: [128 128 3]
         Levels: 1

Merge the two sets of blocks.

blsMerged = mergeBlockLocationSets(bls1,bim,bls2,bim);

Create a blocked image datastore from the merged set of blocks.

bimds = blockedImageDatastore(bim,BlockLocationSet=blsMerged);