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Composite Images

Methods to retrieve Composite images and Thumbnail

  • Composite - Generate an image by compositing Pixel planes into RGB planes.
    • Required Parameters:
      • PixelsID - The Pixels ID of the Pixels that will be used in the composite.
      • theZ - The Z coordinate of the planes.
      • theT - The T coordinate of the planes.
      • One or more RGB channel settings. Each channel's settings are a set of comma separated values which are (in order) the channel index (coordinate in the C dimension), black level, white level, and gamma. Pixel intensities between the specified black level and white level will be scaled from 0 to 255. Intensities above the white level or below the black level will be set to 255 and 0 respectively.
        See the ChannelBasis optional parameter below for different ways of setting the levels.
        The available display channel parameters are:
        • RedChannel
        • GreenChannel
        • BlueChannel
        • GrayChannel
    • Optional Parameters:
      • Format - string (not case-sensitive). The format to return the image in. The currently supported formats are JPG, PNG and TIFF. By default, Format=jpeg
      • LevelBasis - string. This parameter can be used to change the basis of the values used in the white and black levels specified for the display channels (see RGB channel settings above). The LevelBasis can be set to "mean", "geomean' or "absolute". If LevelBasis is "mean", the channel settings are interpreted as standard deviations above (or below if they are negative) the mean pixel intensity for that channel at the given time-point. Similarly, if LevelBasis is "geomean", the channel settings are interpreted as geometric mean-based standard deviations above or below the geometric mean. If LevelBasis is "absolute", the black and white level settings are interpreted as absolute pixel intensities.
        By default, LevelBasis=absolute. If LevelBasis is set to any illegal string, LevelBasis silently (without printing warning or error messages) reverts to absolute.
      • Size - dX,dY. The desired size of the returned image in pixels. The aspect ratio of the image will not change, so the size of the returned image will not exceed the specified size in either dimension, but may be smaller.
        By default, the size of the image returned will be the same size as the pixel dimensions (i.e. the full-size image)
      • SetThumb - any value. If this parameter is present, OMEIS will generate a thumbnail with the specified settings and store it on the server. The Format of the thumbnail will always be JPEG. Nothing is returned if this parameter is set.
      • Save - filename to save as. If this parameter is set, OMEIS will generate a Content-Disposition header set to "attachment" with the filename set to the value of the Save parameter followed by a lower-cased extension with the Format setting (e.g. Save=foo with Format=TIFF will result in the filename "foo.tiff"). The MIME type header will also be set to "application/octet-stream" instead of the proper setting for the specified Format. In most browsers, this will result in the image being saved to the user's disk with the specified filename instead of displayed in a browser window.
    • Return value: The requested image in binary form with the appropriate mime-type.
      Nothing is returned if the SetThumb parameter is present.
    • Example: This command-line example gets a full-size gray-scale TIFF image of the first channel, third Z-section, second timepoint using statistical pixel intensity scaling with the white level set at the mean and the black level set at 4.5 standard deviations above the mean. The TIFF file is saved in myPlane.tiff using the unix shell's output redirection:
                      ./omeis Method=Composite PixelsID=123 theZ=2 theT=1 \
                      LevelBasis=mean GrayChannel=0,0,4.5,1.0 Format=TIFF > myPlane.tiff
  • GetThumb - Get the thumbnail previously defined using the Composite method with the SetThumb parameter.
    • Required Parameters:
      • PixelsID - The Pixels ID of the Pixels that will be read.
    • Optional Parameters:
      • Size - dX, dY. The desired size of the thumbnail in pixels. If the Size parameter is specified, the original pixels will be re-sized to the specified size while using the same pixel intensity scaling and channel mapping specified for the original thumbnail.
    • Return value: The requested thumbnail image in binary form with the image/jpeg mime-type.
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