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I am on ElementaryOS.

To make it simple, I use the shortcut Shift + Print, which allows you to take a custom screenshot (you chose the area of your screen you want to save). I do not want to change the default folder screenshots are saved to. Instead, I would like to chose for each screenshot I take. Is there any way to achieve this?

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One way would be to use the scrot utility to take screenshots. Just pass the full path of the file to be saved in the command line.

You have a number of useful options: you can choose to capture the whole desktop or just the window that has the focus. If you want to manually select the area to capture use the -s option.

So it's quite easy to automate captures and you could even run scrot minimized in a loop with a delay between each capture to speed up your work.

It even does thumbnails and you can also pipe another command.

Scrot: A Command Line Tool to Take Desktop/Server Screenshots Automatically in Linux

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