Processing Commandments for the ZI Scanner

I

Use the appropriate scan resolution

II

Convert the appropriate overview to Spider format

III

DO NOT KEEP MICROGRAPHS ON THE ZI SCANNER

A comparison of the new ZI scanner with the HiScan

ZI scanned files

  • Files may be scanned at different resolutions: 7u (microns), 14u, or larger pixel sizes, in increments of 7u. 7u is the highest resolution. Scanning at lower resolution reduces the scan time as well as the file size. 14u yields approximately the same resolution as the HiScan.For most situations, micrographs should be scanned at 14u. Lower resolution data can still be obtained from these scans (see below).

  • Output scans may be 8-bit (256 gray levels) or 12-bit (4096 gray levels). 12-bit data is actually stored in 16-bit computer words. Micrographs should always be scanned at 12-bits.

  • ZI files can be BIG. A typical micrograph scanned at 14u is 5000 x 6500 12-bit pixels, occupying about 90 Mb (Megabytes). When it's converted to a 4-byte spider file, it will occupy 153 Mb of disk space.

  • ZI scans should be saved in tif format, and given the .tif extension. However, data is arranged in a tiled format which may not be readable by some image viewers. They also have some proprietary header values set aside, e.g., for transmissivity values. The Photoscan software on the ZI computer is the best way to view ZI tif files.

  • ZI files contain a set of increasingly smaller overviews: each successive overview averages 4 pixels into 1 pixel, so the size of the overviews decreases by powers of 2. See Table 1.

    overviews
    from 7u
    scan    		 overviews
    from 14u
    scan    		 width
    (pixels)    		 height
    (pixels)    		 pixelsize
    (Angstrom/pixel)    		 size
    (Mb)
    1 - 11000 15000 1.41 616
    2 1 5500 7000 2.82 153
    3 2 2750 3500 5.64 38
    4 3 1375 1750 11.28 9.5
    5 4 687 875 22.56 2.4
    6 5 346 446 45.12 0.5

    Table 1: SPIDER files converted from ZI overviews



    Note:
    Overview 1 corresponds to the full size image.
    2.82 A pixelsize roughly corresponds to that of HiScan files (2.93 A/pixel).
    Smaller overviews (bigger overview numbers) have better SNR due to averaging of pixels.
    Overview numbers may not correspond to numbers in the Photoscan software.

    Converting ZI files to SPIDER format

    Until a Spider operation such as CP FROM ZI is available, there is a utility on the Unix systems and the ZI PC called zi2spi. It takes a ZI scanned file and an overview number as input, and converts that overview to a Spider file. Pixel values are converted to their density values. It expects as input the original ZI scanned file with a full set of overviews, not an extracted overview or the raw bytes. Usage: 

    zi2spi inputfile outputfile overview#
    For example: 
    zi2spi zi001.tif mic001.spi 2
    will take overview #2 in zi001.tif and convert it to the Spider file mic001.spi. It can also be called from a procedure file using VM: 
    VM
zi2spi zi{***x11}.tif mic{***x11}.spi {*x22}
    *** Note that the extensions of both the ZI and Spider files must be indicated in a VM command. zi2spi is located in /usr/local/spider/bin on Unix machines, and in C:\Program Files\ZI\Common Files on the ZI PC. There is also a procedure file, convert.bat, for converting many files at once.

    Which overview should be converted?

    The smaller the overview,
      - the smaller the resulting file sizes,
      - the faster the processing speed of the Spider operations,
      - the lower the resolution of the final volume.

    Therefore, use the smallest possible overview that will give you the desired final resolution. As a rule of thumb, the best practical resolution you can hope for is 3 times the pixelsize in Table 1.

    Make sure the pixelsize in the parameter file has been set to reflect the extracted overview, not the original scan resolution!

    An alternative approach is to convert the largest overview you will need (highest resolution), then interpolate it down to a smaller size using the IP operation.

    Do not keep micrographs on the ZI scanner

    Files must be transferred to another computer when scanning is completed. Files that have been on the ZI computer over 24 hours will be deleted, without notifying their owner.

    Scanned files should be moved immediately to the Unix file system. Initial analysis can be done on taiwan, the SGI computer in the room across from the ZI scanner (C305B).

    Back to Single Particle Reconstruction

    Source: zidoc.html     Upated: 5/30/01     Bill Baxter

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