Microscopy Image Browser 2.91
MIB
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mibGetImages.m File Reference

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

Functions

function [ img , img_info ] = mibGetImages (files, img_info, options)
 Generate image dataset from the files structure and the img_info containers.Map.
 

Detailed Description

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

Function Documentation

◆ mibGetImages()

function [ img , img_info ] = mibGetImages ( 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)
  • .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
  • .level -> level of the image pyramid to load or an inden within TIF container
    • .xMin -> optional for loading of a region within the image, min X coordinate of the region to load
    • .xMax -> optional for loading of a region within the image, max X coordinate of the region to load%
    • .yMin -> optional for loading of a region within the image, min Y coordinate of the region to load
    • .yMax -> optional for loading of a region within the image, max Y coordinate of the region to load
  • .zMin -> optional for loading of a region within the image, min Z coordinate of the region to load
    • .zMax -> optional for loading of a region within the image, max Z coordinate of the region to load
    • .xyStep -> optional for loading of a region within the image, XY step, pixels between are skipped
img_info-> containers.Map with details of the dataset from getImageMetadata()
options-> structure with options
  • .waitbar -> 0 - no waitbar, 1 - show waitbar
  • .imgStretch [optional] -> stretch or not the image if it is uint32 class
  • .silentMode [optional] -> when true - do not ask questions
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(), max, mibInputMultiDlg(), min, nrrdLoadWithMetadata(), and uint32.

Referenced by mibRechopDatasetController.combineBtn_Callback(), mibAlignmentController.continueBtn_Callback(), mibLoadImages(), and mibWoundHealingAssayController.Stitch().

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