The veteran musician's debut graphic novel will be supported by a soundtrack and iOS app.
Written and illustrated by Johnston, the book will be launched in March at this year's SXSW music festival in Austin.
"This is another instance of bringing it all back home for me personally, because I'm a native of San Antonio and went to school in Austin," said Ross Richie, founder and chief executive officer of BOOM! Studios.
"Daniel is a fixture of the central Texas music scene and an international symbol of the unique creativity the region offers. Getting a chance to work with a seminal voice like Daniel is exactly why I got into publishing in the first place."
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The Space Ducks album features Johnston's first musical output since 2009.
Space Ducks: An Infinite Comic of Musical Greatness will debut on March 13.
Watch a trailer for the 2006 documentary The Devil and Daniel Johnston below: