Question

Why do different regions of cells get coloured differentially

Answer 1

Different dyes show parts of cell in different colour because they bind with the part of cells in specific way and the nature of bond between the staining dye and the parts of the cell varies according to nature of the dye. This variation of way of binding of dyes imparts different colours. Those part of cell which does not bind with dye remain colourless as the staining dye gets washed away during the procedure of staining.
 
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Answer 2

A cell has different chemical composition in different parts. When a stain like Iodine,  saffronine etc. is used,  the different parts of the cell get coloured based on their chemical composition.