title: Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization.
abstract: Current high-resolution imaging techniques require an intact sample that preserves spatial relationships. We here present a novel approach, "puzzle imaging," that allows imaging a spatially scrambled sample. This technique takes many spatially disordered samples, and then pieces them back together using local properties embedded within the sample. We show that puzzle imaging can efficiently produce high-resolution images using dimensionality reduction algorithms. We demonstrate the theoretical capabilities of puzzle imaging in three biological scenarios, showing that (1) relatively precise 3-dimensional brain imaging is possible; (2) the physical structure of a neural network can often be recovered based only on the neural connectivity matrix; and (3) a chemical map could be reproduced using bacteria with chemosensitive DNA and conjugative transfer. The ability to reconstruct scrambled images promises to enable imaging based on DNA sequencing of homogenized tissue samples.
authors.affiliation: Department of Physical Medicine and Rehabilitation, Northwestern University and Rehabilitation Institute of Chicago, Chicago, Illinois, United States of America.
authors.forename: Joshua I
authors.initials: JI
authors.lastname: Glaser
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Bradley M
authors.initials: BM
authors.lastname: Zamft
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.affiliation: Department of Physical Medicine and Rehabilitation, Northwestern University and Rehabilitation Institute of Chicago, Chicago, Illinois, United States of America; Department of Physiology, Northwestern University, Chicago, Illinois, United States of America; Department of Applied Mathematics, Northwestern University, Chicago, Illinois, United States of America.
authors.forename: Konrad P
authors.initials: KP
authors.lastname: Kording
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000166:cytology; D001921:Brain / Q000166:cytology; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional; D008958:Models, Molecular; D057054:Molecular Imaging / Q000379:methods*; D009415:Nerve Net / Q000166:cytology; D009474:Neurons / Q000166:cytology; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA