Microscopy Image Browser  1.233
All Classes Files Functions Variables Pages
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. More...
 

Detailed Description

Read completely the BigDataViewer format of Fiji into Matlab.

Function Documentation

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
filenamename 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
Ia dataset
img_infoimg_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 mib_inputdlg().

Referenced by ib_getImages().

Here is the call graph for this function:

Here is the caller graph for this function: