Fig. 1.

(A) Schematic of all computational steps applied to the experimental replicas. ‘GFP Corrections’ operations are to correct for uneven illumination and detection, dark current, and background fluorescence, and are performed on the stitched composite image of 360 or 396 - FOV. A multi-resolution pyramid representation of each corrected and stitched 2D image was created. Then a set of temporal gigapixel images (which is a terabyte-sized data cube) is stored as a set of pyramids on a server to allow for efficient transmission and viewing of images. (B) Composite image of Oct4-GFP fluorescence of preparation 3 at one time point created by stitching 396 - FOV together into a single composite image. This 16-bit image for this one time point in the fluorescence channel is approximately 1 GB in size. Two colonies are enclosed in boxes and visualized in greater detail in (C). (C) A view of the colonies indicated in the composite image in greater detail using the Deep Zoom tool. Any colony from any image can be viewed in detail via a mouse-click, which produces the colony identification number and data for that colony including coordinates, and features such as average GFP intensity, area, circumference, etc. The full composite image or any subset of it can be panned, visualized in time-lapse mode, and recorded for saving as one or a series of TIFF or PNG files. A video demonstration of the operation of the Deep Zoom visualization tool is provided in Supplemental Movie 1.