Metadata

Store image metadata

Usage

OBJ = Metadata(IMGSIZE, ACQ, CHS, CAL)

Arguments

• IMGSIZE is a vector of the dimensions of the raw image data.
• ACQ is a scalar structure containing information about the image acquisition (e.g. line time, zoom factor etc).
• CHS is a scalar structure that contains information about the meaning of the image channels.
• CAL is a scalar CalibrationPixelSize object.

Details

Metadata objects are used to contain all the extra information (i.e. metadata) about a given raw image. It also implements a number of related helper/convenience functions.

See Also

• Metadata class documentation
• CalibrationPixelSize class documentation
• CalibrationPixelSize quick start guide
• RawImg class documentation
• RawImg quick start guide

Examples

The following examples require the sample images and other files, which can be downloaded manually, from the University of Zurich website (http://www.pharma.uzh.ch/en/research/functionalimaging/CHIPS.html), or automatically, by running the function utils.download_example_imgs().

Create a Metadata object interactively

The following example will illustrate the process of creating a Metadata object interactively. Normally this process is done automatically when creating a RawImg object, but in certain circumstances it is useful to do it manually.

% Call the Metadata constructor
md001 = Metadata()

Answer some questions about the image acquisition. For example, specify that the image was not bidirectional, that the line time was 2ms, and that the zoom factor was 4.

  Please enter a value for if the image is bidirectional [1/0]: 0
  Please enter a value for the line time [ms]: 2
  Please enter a value for the zoom factor: 4

Use the interactive dialogue box to select the dummy calibration (calibration_dummy.mat), which should be located in the subfolder tests>res, within the CHIPS root directory:

We have now created a Metadata object interactively.

md001 =

Warning: The original number of lines per frame is not defined for this
image.  This may be because the metadata was created in an unexpected
way.  Please check carefully any results that depend on the frame rate.
> In Metadata/get.frameRate (line 433)
Warning: The image dimensions are not defined, so the frame rate could
not be determined.
> In Metadata/get.frameRate (line 444)
Warning: The original number of pixels per line is not defined for this
image.  This may be because the metadata was created in an unexpected
way.  Please check carefully any results that depend on the pixel size.
> In Metadata/get.pixelSize (line 469)
Warning: The image dimensions are not defined, so the pixel size could
not be determined.
> In Metadata/get.pixelSize (line 480)

  Metadata with properties:

          calibration: [1x1 CalibrationPixelSize]
             channels: []
   discardFlybackLine: []
            frameRate: NaN
               isBiDi: 0
             lineTime: 2
            nChannels: []
              nFrames: []
       nLinesPerFrame: []
   nLinesPerFrameOrig: []
       nPixelsPerLine: []
   nPixelsPerLineOrig: []
            pixelSize: NaN
            pixelTime: []
                 zoom: 4
        knownChannels: {1x7 cell}

Create a Metadata object without any interaction

% Specify the image dimensions
imgSize = [128, 128, 2, 10];

% Specify some data about the image acquisition
acq = struct('isBiDi', false, 'lineTime', 2, 'zoom', 4, ...
    'nLinesPerFrameOrig', imgSize(1), 'nPixelsPerLineOrig', imgSize(2));

% Specify the channels relevant for this raw image
channels = struct('Ca_Cyto_Astro', 1, 'blood_plasma', 2);

% Load the CalibrationPixelSize object
fnCalibration = fullfile(utils.CHIPS_rootdir, 'tests', 'res', ...
    'calibration_dummy.mat');
calibration = CalibrationPixelSize.load(fnCalibration);

% Create the Metadata object without any interaction
md002 = Metadata(imgSize, acq, channels, calibration)

md002 =
  Metadata with properties:

           calibration: [1×1 CalibrationPixelSize]
              channels: [1×1 struct]
    discardFlybackLine: []
             frameRate: 3.9063
                isBiDi: 0
              lineTime: 2
             nChannels: 2
               nFrames: 10
        nLinesPerFrame: 128
    nLinesPerFrameOrig: 128
        nPixelsPerLine: 128
    nPixelsPerLineOrig: 128
             pixelSize: 2
             pixelTime: []
                  zoom: 4
         knownChannels: {1×7 cell}

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