Extract and display ROIs from a Zeiss CZI image

Version 1.0.0 (3.61 KB) by Peter Nagy
Two programs that extract and display ROIs from Zeiss CZI images.


Updated 24 Mar 2021

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There are two functions in the ZIP file. One of them (extractZeissRois) extracts ROIs from a Zeiss CZI file opened by the bfopen function of Bio-Formats. Information about the ROIs is saved in a structure variable.
The second function (drawZeissRois) draws the ROIs stored in the structure variable.
The displayed image shows eight ROIs in the ZEN program and in an image window in which ROIs extracted and displayed by the two programs in the ZIP file are shown.

function allRois=extractZeissRois(bfImage)
The function extracts ROIs from a Zeiss CZI file opened by Bio-Fomats. The CZI image file must be opened by the 'bfImage' function of Bio-Formats. This is the input to the extractZeissRois function (bfImage). The ROIs are stored in a structure variable (allRois). This structure variable can be used by the drawZeissRois function to display the ROIs.

function roiImage=drawZeissRois(varargin)
The function displays ROIs extracted from a Zeiss CZI file by the extractZeissRois function.
roiImage=drawZeissRois(roiStructure, imageSize, outputType, filled, separateImages)
roiImage=drawZeissRois(roiStructure, imageSize) defaults to 'dipimage' output type, filled ROIs in one image.

roiStructure - a structure variable generated by extractZeissRois
imageSize - a two-element array: [xSize,ySize], i.e. [horizontalSize,verticalSize]
outputType - 'dipimage' or 'matlab' corresponding to a dip_image or a matlab numeric array, respectively
filled - 1 or 0 corresponding to filled ROIs or only their circumference
separateImage - 1 if each ROI is to be saved in a separate image. Otherwise all ROIs will be drawn in the same image.

Cite As

Peter Nagy (2023). Extract and display ROIs from a Zeiss CZI image (https://www.mathworks.com/matlabcentral/fileexchange/89273-extract-and-display-rois-from-a-zeiss-czi-image), MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2020b
Compatible with any release
Platform Compatibility
Windows macOS Linux

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