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Green.h = bigimageshow(bim);showmask(h,bmask,1)title("Mask with Default Inclusion Threshold")To process more blocks of the image, decrease the inclusion threshold.showmask(h,bmask,1,InclusionThreshold=0.4)title("InclusionThreshold = 0.4")You can also process all blocks that have at least a single true pixel in the mask. To use this option, specify the InclusionThreshold name-value argument as 0. Note that not all blocks of the image are included.showmask(h,bmask,1,InclusionThreshold=0)title("InclusionThreshold = 0")Using the mask with any value of InclusionThreshold decreases the total execution time because apply processes only a subset of blocks from the full image. The benefit of using a mask is more significant at higher resolutions and as the processing pipeline increases in complexity.Measure the execution time of filtering the full image.ticbout = apply(bim, ... @(bs)imnlmfilt(bs.Data,DegreeOfSmoothing=15));tFullProcessing = toc;Measure the execution time of filtering only the blocks within the ROI. bls = selectBlockLocations(bim,Mask=bmask,InclusionThreshold=0);ticboutMasked = apply(bim, ... @(bs)imnlmfilt(bs.Data,DegreeOfSmoothing=15), ... BlockLocationSet=bls);tMaskedProcessing = toc;bigimageshow(boutMasked)defaultBlockSize = bim.BlockSize(1,:);title("Processed Image Using Mask with Default BlockSize = [" + ... num2str(defaultBlockSize)+"]");Compare the execution time of processing the full image to the execution time of processing only the blocks in the ROI.disp("Speedup using mask: " + ... num2str(tFullProcessing/tMaskedProcessing) + "x");Speedup using mask: 1.6918xAdjust Block Size to Follow Contours of Region of InterestYou can decrease the block size to create a tighter wrap around the ROI. For some block sizes, this reduces the execution time because apply processes fewer pixels outside the ROI. However, if the block size is too small, then performance decreases because the overhead of processing a larger number of blocks offsets the reduction in the number of pixels processed.Highlight the blocks for apply to process using a smaller block size. To specify the block size, use the BlockSize name-value argument.blockSize = [512 512];h = bigimageshow(bim);showmask(h,bmask,1,BlockSize=blockSize,InclusionThreshold=0)title("BlockSize = [" + num2str(blockSize) + "] | InclusionThreshold = 0")Measure the execution time of filtering all the blocks within the ROI with a decreased block size.bls = selectBlockLocations(bim,Mask=bmask,InclusionThreshold=0);ticboutMasked = apply(bim, ... @(bs)imnlmfilt(bs.Data,DegreeOfSmoothing=15), ... BlockLocationSet=bls);tSmallerBlockProcessing = toc;bigimageshow(boutMasked);title("Processed Image Using Mask with BlockSize = [" + ... num2str(blockSize) + "]");Compare the execution time of processing the entire ROI with smaller blocks to the execution time of processing the entire ROI with the original blocks.disp("Additional speedup using mask with decreased block size: " + ... num2str(tMaskedProcessing/tSmallerBlockProcessing) + "x");Additional speedup using mask with decreased block size: 0.9917x See AlsoblockedImage | bigimageshow | apply Related TopicsDetect and Count Cell Nuclei in Whole Slide Images