A solution depends on what you want to do with the data:
All sparse methods I know are optimized for 2D array manipulations. Therefore I assume, that the creation of the 3D-sparse array will not be the bottleneck for the complete program. If you do not need optimized 2D matrix manipulation methods, you can store the data in a cell array of 2d sparse matrices also, or in one 2D sparse array using a conversion of the indices.
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