Planes

Methods that operate on planes of Pixels

• SetPlane - Write a plane of Pixels.
  • Required Parameters:
    • PixelsID - The Pixels ID of the Pixels that will be written.
    • theZ - The Z coordinate where to start writing pixels.
    • theC - The C coordinate where to start writing pixels.
    • theT - The T coordinate where to start writing pixels.
    • Pixels - The pixels in binary form are sent as a multi-part form in a POST request. The form field must be called "Pixels" and it must be the last part of the form.
      When using the command line, the Pixels parameter doesn't have to be specified. The raw binary pixels are read from stdin.
      The number of pixels sent must exactly match the number of pixels in a plane for the specified set of Pixels.
      The pixels must be in XY order.
  • Optional Parameters:
    • BigEndian - boolean. Set to 0 if the pixels being sent are in little endian byte order. By default, BigEndian=1 (network order)
  • Return value: Number of pixels written

• GetPlane - Get a plane of Pixels.
  • Required Parameters:
    • PixelsID - The Pixels ID of the Pixels that will be read.
    • theZ - The Z coordinate where to start reading pixels.
    • theC - The C coordinate where to start reading pixels.
    • theT - The T coordinate where to start reading pixels.
  • Optional Parameters:
    • BigEndian - boolean. Set to 0 if the pixels should be sent in little endian byte order. By default, BigEndian=1 (network order)
  • Return value: The pixels in binary form in XY order with an application/octet-stream mime-type.

• GetPlaneStats - Get per-plane statistics for all the planes in a set of Pixels.
  • Required Parameters:
    • PixelsID - The Pixels ID of the Pixels that will be read.
  • Return value: The statistics are returned as tab-delimited values with one plane per line in the following column order:

    theC

    theT

    theZ

    min

    max

    mean

    sigma

    geomean

    geosigma

    centroid X

    centroid Y

    sum i

    sum i**2

    sum log(i)

    sum Xi

    sum Yi

    sum Zi

• GetPlaneHist - Get per-plane pixel histogram vector for all the planes in a set of Pixels.
  • Required Parameters:
    • PixelsID - The Pixels ID of the Pixels that will be read.
  • Return value: The statistics are returned as tab-delimited values with one plane per line in the following column order:

    theC

    theT

    theZ

    hist [0]

    hist [1]

    ...

    hist [127]

    The histogram vector is in 128 dimensional space. Its components correspond to bins that uniformly partition the space between min and max. Min and max vary between planes and are the same as returned by GetPlaneStats.

• ConvertPlane - Read a plane of pixels from an uploaded file, and write them to the specified set of Pixels.
  • Required Parameters:
    • PixelsID - The Pixels ID of the Pixels that will be written.
    • FileID - The File ID that the pixels will be read from. The pixels in the file must be in XY order.
    • theZ - The Z coordinate where to start writing pixels.
    • theC - The C coordinate where to start writing pixels.
    • theT - The T coordinate where to start writing pixels.
  • Optional Parameters:
    • Offset - Number of bytes to skip in the file before reading pixels. Useful when the file contains a header, or contains multiple non-contiguous planes. By default, Offset=0.
    • BigEndian - boolean. Set to 0 if the file being converted is in little endian byte order. By default, BigEndian=1 (network order)
    • FlipHorizontal - by default it's set to 0. Set this flag to 1 if the plane should be flipped around its horizontal axis.
  • Return value: The number of pixels converted.

• ConvertTIFF - Read a plane of pixels from an uploaded TIFF file, and write them to the specified set of Pixels. 8, 12, and 16 bit TIFF files are supported.
  • Required Parameters:
    • PixelsID - The Pixels ID of the Pixels that will be written.
    • FileID - The File ID of an uploaded TIFF file that the pixels will be read from.
    • theZ - The Z coordinate where to start writing pixels.
    • theC - The C coordinate where to start writing pixels.
    • theT - The T coordinate where to start writing pixels.
  • Optional Parameters:
    • TIFFDirIndex - Read the plane from the specified TIFF "Directory" when reading multi-plane TIFFs. By default, TIFFDirIndex=0
  • Return value: The number of pixels converted.