loadBigDataViewerFormat.m File Reference

Read completely the BigDataViewer format of Fiji into Matlab. More...

Functions
function [ I , img_info ] =	loadBigDataViewerFormat (filename, options, img_info)
	Read completely the BigDataViewer format of Fiji into Matlab.

Detailed Description

Read completely the BigDataViewer format of Fiji into Matlab.

Function Documentation

loadBigDataViewerFormat()

function [ I , img_info ] = loadBigDataViewerFormat	(		filename,
			options,
			img_info )

Read completely the BigDataViewer format of Fiji into Matlab.

The format description: http://fiji.sc/BigDataViewer#About_the_BigDataViewer_data_format

Parameters

filename	name of the file: xml or h5
options	[optional], a structure with extra parameters .y -> [optional], [ymin, ymax] coordinates of the dataset to take after transpose, height .x -> [optional], [xmin, xmax] coordinates of the dataset to take after transpose, width .z -> [optional], [zmin, zmax] coordinates of the dataset to take after transpose, depth .c -> [optional], [indices] coordinates of the dataset to take after transpose, depth .t -> [optional], [tmin, tmax] coordinates of the dataset to take after transpose, time .level -> [optional], magnification level of the pyramid: 1-for unbinned .waitbar -> [optional] 0 - no waitbar, 1 - show waitbar
img_info	[optional] a container.Maps with details of the dataset obtained from XML file

Return values

I	a dataset
img_info	img_info structure with parameters of the dataset

Required fields of options:

Examples:

[I, img_info] = loadBigDataViewerFormat('mydataset.h5');   // read dataset 

options.x = [50 500];     // define subarea to take
options.y = [50 500];
options.level = 2;        // define level of the image pyramid
[I, img_info] = loadBigDataViewerFormat('mydataset.h5', options);   // load subarea of the dataset 

References max, mibInputDlg(), and min.

Referenced by mibGetImages().

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