I don't think you can do it if the tree spans multiple cells like it is in your picture. By cells I mean the orange squares.
In the TileSet window on the bottom of the screen, select your trees atlas (the thing labelled "TX Plant.png (ID: 5)") and in the atlas properties adjust the Texture Resolution to be the size of each tree. This will be the same size for all tree sprites, so make is the size of the largest tree. You should have 3 large, rectangular cells that contain each tree. The trees shouldn't be split across multiple cells.
Then,
Go to Tile Properties (the cursor icon right of the Atlas Properties icon) and for each cell adjust Texture_Offset property under Rendering. This means you can move where the base of the tree is in the sprite so that it is placed how you want.