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Is there any software out there on the internet, preferably free, that can turn a large amount of images into transparent gifs (Assuming that all these files have the same background color that I want to set transparent)?

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Use IrfanView. Batch convert the file to .gif, and in the format options menu, check the 'Save Transparent GIF option'.

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Thanks Irfan25FF :D –  dpek May 23 '10 at 16:31

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