BioFormats

Store raw data from BioFormats images

Usage

OBJ = BioFormats(FILENAME, CHS, CAL)

Arguments

• FILENAME is the original filename (including the path) of this BioFormats object.
• CHS is a scalar structure that contains information about the meaning of the image channels.
• CAL is a scalar CalibrationPixelSize object.

Details

BioFormats objects are used to contain all raw image data and metadata from Bio-Formats Tif images. This class relies on existing code from the Bio-Formats library. For more information, please visit http://www.openmicroscopy.org/site/products/bio-formats.

See Also

• RawImg class documentation
• Metadata class documentation
• Metadata quick start guide
• CalibrationPixelSize class documentation
• CalibrationPixelSize 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().

In addition, loading Bio-Formats images requires prior installation of the Bio-Formats Java library, which can be downloaded manually from the Open Microscopy Environment website (‘http://www.openmicroscopy.org/site/products/bio-formats), or automatically by running the function utils.install_bfmatlab().

Create a BioFormats object interactively

The following example will illustrate the process of creating a BioFormats object interactively. It is possible to do so by using the from_files() method, rather than the constructor (as is demonstrated in this section).

% Call the BioFormats constructor
bf001 = BioFormats()

Use the interactive dialogue box to select the raw image file cellscan_ome_tiff.ome.tif.

The next stage is to define the ‘meaning’ of the image channels. The first channel represents a cytosolic calcium sensor expressed in astrocytes. Press three and then enter to complete the selection.

----- What is shown on channel 1? -----

  >> 0) <blank>
     1) blood_plasma
     2) blood_rbcs
     3) Ca_Cyto_Astro
     4) Ca_Memb_Astro
     5) Ca_Neuron
     6) cellular_signal
     7) FRET_ratio

Answer: 3

We have now created a BioFormats object interactively.

bf001 =

BioFormats with properties:

            filename: 'C:\...'
          isDenoised: 0
   isMotionCorrected: 0
   metadata_original: [1x1 loci.formats.ome.OMEXMLMetadataImpl]
                name: 'cellscan_ome_tiff.ome'
             rawdata: [4-D uint16]
                  t0: 0
            metadata: [1x1 Metadata]

The process is almost exactly the same to create an array of BioFormats objects; when the software prompts you to select one or more raw images, simply select multiple images by using either the shift or control key.

Create a BioFormats object without any interaction

% Specify the full path to the raw image object
fnST002 = fullfile(utils.CHIPS_rootdir, 'tests', 'res', ...
    'cellscan_ome_tiff.ome.tif');

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

% Create the SCIM_Tif object without any interaction
bf002 = BioFormats(fnST002, channels);

% View the SCIM_Tif object
bf002.plot()

Reading series #1
    ....................

Home