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CHIPS

Cellular and Hemodynamic Image Processing Suite

CalibrationPixelSize

Store pixel size calibration

Usage

OBJ = CalibrationPixelSize(ZOOM, PXSIZE, IMGSIZE, OBJECTIVE, DATE,
    NAME, PERSON, FUNRAW)

Arguments

Details

CalibrationPixelSize contains a calibration relating a given microscope zoom factor to a known physical pixel size (in units of distance) for a given objective.

See Also

Examples

Create a CalibrationPixelSize object

The following example will illustrate the process of creating a CalibrationPixelSize object. Normally this process only needs to be done once per objective/microscope combination.

% Specify some zoom values
zoom = 2.^(0:5)

% Specify some values for pixel size at the defined zoom, with added noise
pxSize = (1./zoom).*(1 + 0.05*randn(1, numel(zoom)))

% Specify the original number of pixels in the calibration images
imgSize = 256;

% Specify some other aspects of the calibration
objective = 'imaginary';
date = 'yesterday';
name = 'test calibration';
person = 'Dr Who';
funRaw = @CalibrationPixelSize.funRawHyperbola;

% Call the CalibrationPixelSize constructor
cal001 = CalibrationPixelSize(zoom, pxSize, imgSize, objective, date, ...
    name, person, funRaw)

% Show a plot of the calibration. (Note: your image may differ due to the
% random data used to generate the calibration)
cal001.plot();

zoom =
     1     2     4     8    16    32
pxSize =
    0.9548    0.5306    0.2376    0.1137    0.0596    0.0294
cal001 =
  CalibrationPixelSize with properties:

         date: 'yesterday'
       funRaw: @CalibrationPixelSize.funRawHyperbola
      imgSize: 256
         name: 'test calibration'
    objective: 'imaginary'
       person: 'Dr Who'
    pixelSize: [6×1 double]
         zoom: [6×1 double]

IMAGE

Saving a CalibrationPixelSize object

% Save the calibration
cal001.save('cal001.mat');

Loading a CalibrationPixelSize object

% Load the calibration
cal001_reloaded = CalibrationPixelSize.load('cal001.mat')

% Check that the loaded calibration is the same as the one we saved
isEqual = cal001 == cal001_reloaded

cal001_reloaded =
  CalibrationPixelSize with properties:

         date: 'yesterday'
       funRaw: @CalibrationPixelSize.funRawHyperbola
      imgSize: 256
         name: 'test calibration'
    objective: 'imaginary'
       person: 'Dr Who'
    pixelSize: [6×1 double]
         zoom: [6×1 double]
isEqual =
  logical
   1

Creating a 'dummy' CalibrationPixelSize object

The following example will illustrate the process of creating a ‘dummy’ CalibrationPixelSize object. This process is needed to specify the pixel size for images that do not possess the necessary metadata to create their own calibration (as normally happens with BioFormats images) or use a calibration based on the zoom value (as normally happens with SCIM_Tif images).

% Specify the desired pixel size
pxSizeImg = 1.234; % um

% Specify the image size.  This is important to set correctly, because the
% pixel size for an image depends on both the calibration and the image
% size.  For example, for the same calibration, a 128 x 128 pixel image
% will have a pixel size two times larger than a 256 x 256 pixel image.
imgSizeDummy = 256;

% Specify the remaining information
zoomDummy = [1 100];
pxSizeDummy = pxSizeImg.*ones(size(zoomDummy));
objectiveDummy = 'dummy';
dateDummy = 'dummy';
nameDummy = 'dummy';
personDummy = 'dummy';
funRawDummy = @CalibrationPixelSize.funRawDummy;

% Create the calibration object
calDummy = CalibrationPixelSize(zoomDummy, pxSizeDummy, imgSizeDummy, ...
    objectiveDummy, dateDummy, nameDummy, personDummy, funRawDummy);

% Show the pixel size that will be returned
zoom05 = 5;
pxSize05_1 = calDummy.calc_pixel_size(zoom05, imgSizeDummy)

pxSize05_1 =
    1.2340


% Note that the pixel size is different for different image sizes
pxSize05_2 = calDummy.calc_pixel_size(zoom05, imgSizeDummy/2)

pxSize05_2 =
    2.4680


% For dummy calibrations, the pixel size is the same for all zoom values
zoomRange = 1:10:100;
pxSize05_range = calDummy.calc_pixel_size(zoomRange, imgSizeDummy)

pxSize05_range =
  Columns 1 through 7
    1.2340    1.2340    1.2340    1.2340    1.2340    1.2340    1.2340
  Columns 8 through 10
    1.2340    1.2340    1.2340

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