How to replace multiple values in an large array with the occurrence of the value?

General Usage
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4

You need to iterate the array keeping the column-major layout in mind. map! would do this for you. You may also loop over the array by yourself:

julia> using StatsBase

julia> blobs = rand(1:10, 10_000, 10_000);

julia> blobs_occ = countmap(vec(blobs))
Dict{Int64,Int64} with 10 entries:
  7  => 9999281
  4  => 10004145
  9  => 9998303
  10 => 10000867
  2  => 10003930
  3  => 10000831
  5  => 10001701
  8  => 9993679
  6  => 9996181
  1  => 10001082

julia> blob_counts = similar(blobs);

julia> function elcount!(blob_counts, blobs, blobs_occ)
           for (ind, el) in enumerate(blobs)
               blob_counts[ind] = blobs_occ[el]
           end
           return blob_counts
       end

julia> @time elcount!(blob_counts, blobs, blobs_occ);
  1.499894 seconds
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