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readBigDataViewerFormat.m File Reference

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

Functions

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

Detailed Description

Read completely the BigDataViewer format of Fiji into Matlab.

Function Documentation

function [ img_info , I ] = readBigDataViewerFormat (   filename,
  orient,
  options 
)

Read completely the BigDataViewer format of Fiji into Matlab.

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

Parameters
filenamename of the file: xml or h5
orient[optional], can be NaN
  • when 0 (default) returns the dataset transposed to the current orientation (obj.orientation)
  • when 1 returns transposed dataset to the zx configuration: [y,x,c,z,t] -> [x,z,c,y,t]
  • when 2 returns transposed dataset to the zy configuration: [y,x,c,z,t] -> [y,z,c,y,t]
  • when 3 not used
  • when 4 returns original dataset to the yx configuration: [y,x,c,z,t]
  • when 5 not used
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
Return values
img_infocontainers.Map with metadata
I[optional], a dataset
Required fields of options:

Examples:

img_info = readBigDataViewerFormat('mydataset.xml'); // read only metadata
img_info = readBigDataViewerFormat('mydataset.h5'); // read only metadata directly from hdf5 dataset
[img_info, I] = readBigDataViewerFormat('mydataset.xml'); // read both metadata and dataset

References xml2struct().

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