Microscopy Image Browser  1.233
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ib_getImages.m File Reference

Generate image dataset from the files structure and the img_info containers.Map. More...

Functions

function [ img ,

img_info ] = 
ib_getImages (files, img_info, options)
 Generate image dataset from the files structure and the img_info containers.Map. More...
 

Detailed Description

Generate image dataset from the files structure and the img_info containers.Map.

Function Documentation

function [ img , img_info ] = ib_getImages (   files,
  img_info,
  options 
)

Generate image dataset from the files structure and the img_info containers.Map.

Parameters
files- > structure from getImageMetadata.m
  • .object_type -> type of the data, 'movie', 'hdf5_image', 'image'
  • .filename - filenames
  • .seriesName -> name of the series for HDF5/Bioformats
  • .height -> image height
  • .width -> image width
  • .color -> number of color channels
  • .noLayers -> number of image slices in the file
  • .imgClass -> class of the image, 'uint8','uint16'...
  • .dim_xyczt -> dimensions for hdf5_image and Bioformats, AmiraMesh (binned version)
  • .hDataset -> handle to Bioformats dataset
  • .depth_start - > [optional], for Amira Mesh only, to take only specified sections
  • .depth_end - > [optional], for Amira Mesh only, to take only specified sections
  • .depth_step -> [optional], for Amira Mesh only, Z-step to take not all sections
  • .xy_step -> [optional], for Amira Mesh only, XY-step, i.e. binning factor
  • .resizeMethod -> [optional], for Amira Mesh only, resize method for binning the XY-dimension, 'nearest', 'bilinear', 'bicubic'
  • .backgroundColor -> [optional], to define a color when generating a stack from images of different XY dimensions. Only files(1).background is needed
img_info-> containers.Map with details of the dataset from getImageMetadata()
options-> structure with options
  • .waitbar -> 0 - no waitbar, 1 - show waitbar
Return values
img-> image dataset [1:height, 1:width, 1:color, 1:z]
img_info-> modified containers.Map with details of the dataset
Required fields of options:

References amiraMesh2bitmap(), loadBigDataViewerFormat(), and nrrdLoadWithMetadata().

Referenced by ib_loadImages(), mibDriftAlignDlg>continueBtn_Callback(), and mibrechopDatasetGui>combineBtn_Callback().

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