Yes. Gamemaker can import .png files, and allows you to import spritesheets as well. This tutorial video shows the process :
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I checked the original files and the ships are not layered, so the coloured part is not separate. It's possible through photoshop to extract the coloured parts and save them separately. But this loses some of the subtle detail in the coloured sections, so the result doesn't look as good as the hue shift mechanism I mentioned in my earlier reply.
If you're familiar with photoshop (though I assume most graphics software packages offer something similar), you'd be recreating the 'hue/saturation' effect, in Krita it's called 'HSV/HSL Adjustment'. See attached image.
I'll have to dig up my original files from backup to answer this, but I think not. However, I'll confirm soon.
That said, I remember from when I made games myself it was possible to change only the non-grey parts of an image. The process was called 'hue shift' or 'hue rotate' - it's been a while so I'm afraid that's all I remember.
Yes, you are allowed to distribute and sell your game. You're also allowed to edit these to fit your project.
The only restriction is that one may not re-sell or distribute the assets by themselves, be it individual images or the entire set - the images need to be part of a larger project, like a game.
I have two other sets on itch.io in isometric fashion : https://nulllgames.itch.io/isometric-military-vehicles and https://nulllgames.itch.io/isometric-spaceship-sprites
The Indoor set has 2928 image files. I don't have a file handy that shows a full index, but I've made a screenshot of the entire folder : http://nulll.net/assets/previews/
Anything in particular you wish to know more details about?
I have several sets in the works as well : an outdoors set with the same dimensions and style as the Medieval indoor tiles and a set of fantasy characters (knights, wizards, etc) also matching the indoor and outdoor tiles.
I'm also working on contemporary city sets with houses, cars, street tiles, etc, but no ETA on any of these sets.
I've done custom work before, here's an image of a set for a war-themed game :