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Import 3D Image Stack (ImageProcessing)

Group (Subgroup)

IO (Input)

Description

This Filter is used to import a stack of 2D images that represent a 3D volume. This Filter makes use of ITK's classes to perform the import. In theory the filter should be able to import any type of image supported by ITK. Due to the nature of file systems and the strict lexicographical sorting of most file system APIs the user needs to enter parameters that will allow DREAM.3D to actually generate the file names and then check if those files actually exist. This approach guarantees that the images will be ordered correctly in the Z Direction within the 3D array.

Visualization Notes

Note that due to limitations of the Xdmf wrapper, 4 component ARGB images cannot be visualized using ParaView. The only current way to solve this issue is to import the image data and then apply the Flatten Image Filter, which will convert the color data to gray scale data. The image can then be visualized in ParaView using the Xdmf wrapper.

Importing a Stack of Images

This Filter will import a directory of sequentially numbered image files into the DREAM.3D data structure, creating a Data Container, Cell Attribute Matrix, and Attribute Array in the process, which the user may name. The user selects the directory that contains all the files to be imported then uses the additional input widgets on the Filter interface (File Prefix, File Suffix, File Extension, and Padding Digits) to make adjustments to the generated file name until the correct number of files is found. The user may also select starting and ending indices to import. The user interface indicates through red and green icons if an expected file exists on the file system. This Filter may also be used to import single images in addition to stacks of images.
The user has the option to read the images in as an Image Geometry or a Rectilinear Grid Geometry. If the user chooses Image Geometry, then the origin and resolution of the imported images must be entered. The resolution (or size of the Cells) is the same for all Cells in this case. If the user chooses Rectilinear Grid Geometry, then a file path to a file that lists the bounds of Cells in the X, Y and Z directions must be provided. The format of the file is provided below. Note that the bounds array for each direction will be the number of Cells in that direction plus 1 (i.e., a 100x90x80 Cell dataset will have 101x91x81 bounds values).

# Comment line
# Comments can start with the '#' character
X_COORDINATES [number of X coordinates] 
x0 x1 ... x(nx-1)
Y_COORDINATES [number of Y coordinates] 
y0 y1 ... y(ny-1)
Z_COORDINATES [number of Z coordinates] 
z0 z1 ... z(nz-1)

Import Image Stack User Interface @image latex ExampleGUI.png "Import Image Stack User Interface" width=6in

Example Stack Import

MNML-3_200x_769-Raw_p09_Aligned.tif
MNML-3_200x_770-Raw_p09_Aligned.tif
MNML-3_200x_771-Raw_p09_Aligned.tif
MNML-3_200x_772-Raw_p09_Aligned.tif
MNML-3_200x_773-Raw_p09_Aligned.tif
MNML-3_200x_774-Raw_p09_Aligned.tif
MNML-3_200x_775-Raw_p09_Aligned.tif
MNML-3_200x_776-Raw_p09_Aligned.tif
MNML-3_200x_777-Raw_p09_Aligned.tif
MNML-3_200x_778-Raw_p09_Aligned.tif
MNML-3_200x_779-Raw_p09_Aligned.tif
MNML-3_200x_780-Raw_p09_Aligned.tif
Parameter Value
File Prefix MNML-3_200x_
File Suffix -Raw_p09_Aligned
File Extension tif
Start Index 769
End Index 780
Padding Digits 3

DREAM.3D contains numerous tools to modify, analyze and segment generic image data. If your images are already pre-processed so that they are segmented into specific regions, DREAM.3D may also be able to work with the image data and produce meaningful results. Three categories of images that DREAM.3D can handle include the following:


Category 1 Image

The regions of the image that represent an Ensemble or Feature each have a unique identifier such as a grayscale value or unique RGB value.

Category 1 Image @image latex Images/Type1.png "Category 1 Image" width=6in


Category 2 Image

There are regions in the image that represent Features, where each region has a unique identifier but there are multiple regions with the same identifier.

Category 2 Image @image latex Images/Type2.png "Category 2 Image" width=6in


Category 3 Image

Each Feature is traced out via another pixel identifier so that Feature boundaries are "black" and each Feature is "white". This type of image is commonly referred to as a binary image.

Category 3 Image @image latex Images/Type3.png "Category 3 Image" width=6in


Note that the above categories represent a small subset of the kinds of images DREAM.3D can process. In general, any kind of multi-dimensional data can be stored and analyzed by DREAM.3D.

Parameters

See Description

Required Geometry

Not Applicable

Required Objects

None

Created Objects

Kind Default Name Type Component Dimensions Description
Data Container ImageDataContainer N/A N/A Created Data Container name with an Image Geometry
Attribute Matrix CellData Cell N/A Created Cell Attribute Matrix name
Cell Attribute Array ImageData uint8_t (n) Attribute Array for the imported image data. The dimensionality of the array depends on the kind of image read: (1) for grayscale, (3) for RGB, and (4) for ARGB

Example Pipelines

Please see the description file distributed with this Plugin

DREAM.3D Mailing Lists

If you need more help with a Filter, please consider asking your question on the DREAM.3D Users Google group!