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CHIPS

Cellular and Hemodynamic Image Processing Suite

Other Preprocessing Utilities

A number of other preprocessing utilities are included in the CHIPS toolbox. For example, it is possible to calculate a new channel using information from other channels (e.g. for FRET ratiometric sensors), to split images up into multiple smaller images, and to concatenate images together.

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().

Prepare a `RawImg` for use in these examples

% Prepare a rawImg for use in these examples
fnRawImg = fullfile(utils.CHIPS_rootdir, 'tests', 'res', ...
    'xsectscan_scim.tif');
channels = struct('cellular_signal', 1, 'blood_plasma', 2);
fnCalibration = fullfile(utils.CHIPS_rootdir, 'tests', 'res', ...
    'calibration_dummy.mat');
calibration = CalibrationPixelSize.load(fnCalibration);
rawImg = SCIM_Tif(fnRawImg, channels, calibration);

Opening xsectscan_scim.tif: 100% [=================================]

Calculate a ratio channel

% Make a copy of the RawImg object so we can reuse the original later
ri001 = copy(rawImg);
nChs_pre = ri001.metadata.nChannels

% Calculate a ratio channel (i.e. ch3 = ch1 ./ ch2)
chNums = [1, 2];
chName = 'cellular_signal';
ri001.ch_calc_ratio(chNums, chName);
nChs_post = ri001.metadata.nChannels

nChs_pre =
     2
nChs_post =
     3

Split the image into separate channels

% Split the image into separate channels
ri002 = copy(rawImg);
dim = 3;
dimDist = [1, 1];
[ri002_ch1, ri002_ch2] = ri002.split1(dim, dimDist);
ch1_name = ri002_ch1.metadata.get_ch_name(1)
ch2_name = ri002_ch2.metadata.get_ch_name(1)

ch1_name =
  cell
    'cellular_signal'
ch2_name =
  cell
    'blood_plasma'

Concatenate multiple images together

% Concatenate multiple images together (including recursively)
nFrames_pre = rawImg.metadata.nFrames
dim = 4;
riArray(1:3) = copy(rawImg);
ri003 = RawImg.cat_data(dim, copy(rawImg), riArray, copy(rawImg));
nFrames_post = ri003.metadata.nFrames

nFrames_pre =
    50
nFrames_post =
   250

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