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Do the objects have to be that small ? For instance you can use lines instead of dots and show more information when hoover. The area of selection gets way bigger since it does not depend on Y and X axis but on X only.

Let the user select a container box. Then system should make the first object in that box as current object and highlight it (as we do highlight current list item). User should be able to move through the objects using left arrow and right arrow keys of keyboard or by clicking on the arrow buttons provided on either side of the selected container box. ...

One solution is to show a magnified version directly above where the user is currently hovering. Look at how YouTube deals with seeking long videos, for example: This allows the user to select a rough time period they are interested in, then make a finer selection using the shorter-interval magnification. The Music app on the iPhone/iPod has a feature ...