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Description
While on your animation program, make it so that the background, usually the bottom layer, isn't visible. On GIMP or Photoshop, for example, you would click the eye icon on the bottom layer to take away visibility. Once you do that just save the picture as a PNG or GIF, not a JPG, XCF, PSD, etc.

Example:
I saved this picture as adoptable4, so this is what I did:
I clicked 'save as' under file.
I saved it as: adoptable4.PNG

I saved this from Photoshop, but I've done it from GIMP before so I know about little popups. You shouldn't worry about merge or merge level. They don't matter much - if at all- so don't sweat it. Interlace usually doesn't make any difference either.

Really hope that wasn't as confusing as I think it is.
I tried my best to explain everything.

SAI users

I used to be able to, while in SAI, simply save the picture as a PNG file and have the option to give all visible pixels opactity or something. I don't remember, because for some reason it won't give the option anymore. You can still achieve a transparent BG though.

Export the drawing as a PSD (Photoshop) file. If you don't know how to do that, the export option is simply under file. After you export it, you can open it again in Photoshop and just following the instructions above. Easy! I think. oAo''

You could export the drawing as an XCF file, too, and do the same in GIMP.

Description
While on your animation program, make it so that the background, usually the bottom layer, isn't visible. On GIMP or Photoshop, for example, you would click the eye icon on the bottom layer to take away visibility. Once you do that just save the picture as a PNG or GIF, not a JPG, XCF, PSD, etc.

Example:
I saved this picture as adoptable4, so this is what I did:
I clicked 'save as' under file.
I saved it as: adoptable4.PNG

I saved this from Photoshop, but I've done it from GIMP before so I know about little popups. You shouldn't worry about merge or merge level. They don't matter much - if at all- so don't sweat it. Interlace usually doesn't make any difference either.

Really hope that wasn't as confusing as I think it is.
I tried my best to explain everything.

SAI users

I used to be able to, while in SAI, simply save the picture as a PNG file and have the option to give all visible pixels opactity or something. I don't remember, because for some reason it won't give the option anymore. You can still achieve a transparent BG though.

Export the drawing as a PSD (Photoshop) file. If you don't know how to do that, the export option is simply under file. After you export it, you can open it again in Photoshop and just following the instructions above. Easy! I think. oAo''

You could export the drawing as an XCF file, too, and do the same in GIMP.