This page contains a Flash digital edition of a book.
Web-Based Interactive Measurements


Figure 4 : Stitched images of small FOVs without fl at fi eld correction (top left) and after fl at fi eld correction (bottom left). Both images on the left have been contrast- enhanced via histogram equalization on the right side to show the differences. Each FOV image is 3,072 × 2,048 pixels (148.992 × 99.328 micrometers). The stitched image is 223,836 × 122,577 pixels (10.856 × 5.945 millimeters).


to optimize, validate, and verify results of automated parame- terized computations. Figure 1 illustrates user interactions with the web system and the steps in the processing assembly part of this client-server system.


1. Upload user interface (UI): A user can drag and drop folders with files or individual files one by one to a browser UI to upload image collections. File types are automatically classifi ed as image or text based on their suffi x (MIME type). 2. Large FOV assembly: The assembly of a large FOV requires a sequence of computational steps running on the server (top of Figure 1 ). T e type of input images (small FOVs) determines the choice of steps and their order. A user is able to set up parameters via one or more user interfaces in a browser and launch computational steps in any order as long as input/ output data types match. T e minimum number of computa- tional steps includes (1) the estimation of a stitching vector containing the global image tile positions for all the small FOVs, (2) intensity scaling if the acquired small FOV intensities range outside of 0 to 255, and (3) multi-resolution pyramid building. T e intensity scaling is necessary because current browsers only support images with 8 bits per pixel. T e image pyramid shown in Figure 2 is constructed to avoid limitations of typical network resources. The pyramid representation is useful


2017 January • www.microscopy-today.com


for transmitting to end users only the portions of the image that are being viewed. In addition to enabling interactive pan-zoom viewing, the pyramid construction from small FOVs also avoids the challenges associated with constructing one large multi-giga-pixel fi le that might not fi t to RAM. Additional computational steps can be launched as needed. All available computations are listed in Table 1 . All metadata coming from microscope acquisitions and intermediate workfl ow computations are hyperlinked with the resulting data, as computational steps are applied to assemble a large FOV. T e metadata are stored following the Open Microscopy Environment (OME) fi le format (OME Data Model, OME-XML, and OME-TIFF) and allow traceability of the results to data acquisition and computational steps. Figure 3 illustrates user access to either Data types or computational Jobs listed in Table 1 via the drop-down menus. T e fi gure also shows measurement tools and an interactive pan-zoom view of one large FOV that was selected from the resulting Data types. 3. Interactive viewing and exploration of large FOV: Interactive viewing is based on transferring pyramid images from a server to a client according to a user-chosen level of detail (zoom) and spatial location (pan). Multi-resolution image pyramids have been previously used in the context of “Virtual Microscopy” [ 3 ] as effi cient representations for transmission and


21


Page 1  |  Page 2  |  Page 3  |  Page 4  |  Page 5  |  Page 6  |  Page 7  |  Page 8  |  Page 9  |  Page 10  |  Page 11  |  Page 12  |  Page 13  |  Page 14  |  Page 15  |  Page 16  |  Page 17  |  Page 18  |  Page 19  |  Page 20  |  Page 21  |  Page 22  |  Page 23  |  Page 24  |  Page 25  |  Page 26  |  Page 27  |  Page 28  |  Page 29  |  Page 30  |  Page 31  |  Page 32  |  Page 33  |  Page 34  |  Page 35  |  Page 36  |  Page 37  |  Page 38  |  Page 39  |  Page 40  |  Page 41  |  Page 42  |  Page 43  |  Page 44  |  Page 45  |  Page 46  |  Page 47  |  Page 48  |  Page 49  |  Page 50  |  Page 51  |  Page 52  |  Page 53  |  Page 54  |  Page 55  |  Page 56  |  Page 57  |  Page 58  |  Page 59  |  Page 60  |  Page 61  |  Page 62  |  Page 63  |  Page 64  |  Page 65  |  Page 66  |  Page 67  |  Page 68