11.79. Read Fiji Montage (ITK)
Imports a set of overlapping tile images described by a Fiji/ImageJ TileConfiguration file, placing each tile in its own data group for later montage assembly.
Group (Subgroup)
IO (Input)
Description
This filter reads a Fiji/ImageJ TileConfiguration file and imports the overlapping tile images it references so they can later be assembled into a single montage. The configuration file lists each tile image along with the coordinate at which it belongs in the mosaic. The image files must be located in the same directory as the configuration file.
Each tile is imported into its own Image Geometry, named using the Image Geometry Prefix followed by the tile’s file name. Inside each Image Geometry, the pixel data is stored in a Cell Attribute Matrix group, which holds the image Data Array. If Parent Imported Images Under a DataGroup is enabled, all of these per-tile Image Geometries are placed under a single parent DataGroup so they are grouped together in the DataStructure.
Use this filter as the first step in a montage-stitching workflow when your tiles are described by a Fiji TileConfiguration file.
Parameter Guidance
Change Origin / Origin — when enabled, overrides the origin of the assembled mosaic with the user-supplied value (in the chosen length unit).
Convert To GrayScale / Color Weighting — when enabled, converts color tiles to grayscale using a weighted (luminosity) average of the red, green, and blue channels. The default weights are the BT.709 values Red 0.2125, Green 0.7154, Blue 0.0721, which approximate human brightness perception (the eye is most sensitive to green). The weights can be changed to any values. The incoming color array must be 8-bit unsigned (uint8); otherwise that image is skipped.
Set Image Data Type / Output Data Type — when enabled, stores the imported pixel data using the chosen numeric type (uint8, uint16, or uint32).
Length Unit — the physical length unit applied to the created Image Geometries.
Required Input Sources
A Fiji/ImageJ TileConfiguration text file, with all referenced tile images in the same directory.
Example Configuration File
# Define the number of dimensions we are working on
dim = 2 <===== THIS LINE IS REQUIRED
# Define the image coordinates <===== THIS LINE IS REQUIRED
SampleMosaic_p0.bmp; ; (0, 0)
SampleMosaic_p1.bmp; ; (1227.55, 0)
SampleMosaic_p3.bmp; ; (0.23675, 920.01)
SampleMosaic_p2.bmp; ; (1227.55, 919.774)
SampleMosaic_p4.bmp; ; (0.23675, 1839.55)
SampleMosaic_p5.bmp; ; (1227.31, 1839.55)
Input Parameter(s)
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Fiji Configuration File |
FileSystemPath |
This is the configuration file in the same directory as all of the identified geometries |
|
Length Unit |
Choices |
The length unit that will be set into the created image geometry |
|
Change Origin |
Bool |
Set the origin of the mosaic to a user defined value |
|
Origin |
Vector of Float32 Values |
Order=,, |
The new origin of the mosaic |
Convert To GrayScale |
Bool |
The filter will show an error if the images are already in grayscale format |
|
Color Weighting |
Vector of Float32 Values |
Order=,, |
The luminosity values for the conversion |
Set Image Data Type |
Bool |
Set the final created image data type. |
|
Output Data Type |
Choices |
Numeric Type of data to create |
|
Parent Imported Images Under a DataGroup |
Bool |
Create a new DataGroup to hold the imported images |
Output Data Object(s)
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Name of Created DataGroup |
String |
Name of the overarching parent DataGroup |
|
Image Geometry Prefix |
String |
A prefix that can be used for each Image Geometry |
|
Cell Attribute Matrix Name |
String |
The name of the Cell Attribute Matrix |
|
Image DataArray Name |
String |
The name of the import image data |
Example Pipelines
Prebuilt Pipelines / Examples / ITKImageProcessing / Fiji Import
License & Copyright
Please see the description file distributed with this Plugin
DREAM3D-NX Help
If you need help, need to file a bug report or want to request a new feature, please head over to the DREAM3DNX-Issues GitHub site where the community of DREAM3D-NX users can help answer your questions.