Transparent colors in .bams... OR converting .png into .bams

The EE additions included a bunch of new items with hand-drawn item art in .png format, allowing for high quality images like this and this without having pixelation or out of place colors. Any idea how to replicate this with custom images? Even copying existing .bams causes transparent colors to become erased. Knowing how to convert .png images would help in making custom description images look a lot better.