Figure 1

Optical mapping system. An overview of the optical mapping system. A; Large, genomic DNA molecules are elongated and arrayed as 15 mm long stripes onto positively charged surfaces using a microfluidic device; a green line depicts one channel (48 total). B; After restriction digestion and staining, an automated fluorescence microscope scanner ("Genome Zephyr"; [D]) serially acquires overlapping image frames along each of the 48 stripes laid down by the microfluidic device. ChannelCollect software flattens and overlaps images maintaining sub-pixel registration; ~8/170 overlapped image frames from one channel are shown. White "threads" are individual DNA molecules; blue boxes indicate each ~100 μm-wide frames. C; Machine vision (Pathfinder [32, 33]) identifies molecules and constructs ordered restriction maps for each molecule; integrated fluorescence intensity measurements estimate mass of daughter restriction fragments in kilobasepairs. D; An optical mapping station known as Genome Zephyr; pictures show microscope, fiber-optic illumination, computer controlled stage. The insert shows the optical mapping software interface–ChannelCollect. The user identifies the start and end coordinates of the first and last channel on a surface. Further channels are identified by the software. Imaging and data processing are fully automated.