9.79. Read Fiji Montage (ITK)

Group (Subgroup)

Import/Export (Import)

Description

Imports multiple images for the purpose of montage assembly. Each image is stored in it’s own DataContaner/AttributeMatrix/AttributeArray where the name of the DataContainer is based off the row & column index of the montage. The filter assumes that the Configuration File is in the same folder as the images. The created AttributeMatrix and AttributeArray will have the same name. The image files MUST be located in the same directory as the Fiji Configuration File.

Utilizes the itkReadImage and ColorToGrayScale filters

Example Registration 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)

Color To Gray Scale Notes

For this option to work the read in color array must be a UInt8Array otherwise the image will be skipped over when loading

The luminosity method is a more sophisticated version of the average method. It also averages the values, but it forms a weighted average to account for human perception. We re more sensitive to green than other colors, so green is weighted most heavily. The default formula for luminosity is BT709 Gray scale:

Red: 0.2125 Green: 0.7154 Blue: 0.0721.

The user can set the weightings to what ever values they would like.

Lenght Unit

Yoctometer = 0
Zeptometer = 1
Attometer = 2
Femtometer = 3
Picometer = 4
Nanometer = 5
Micrometer = 6
Millimeter = 7
Centimeter = 8
Decimeter = 9
Meter = 10
Decameter = 11
Hectometer = 12
Kilometer = 13
Megameter = 14
Gigameter = 15
Terameter = 16
Petameter = 17
Exameter = 18
Zettameter = 19
Yottameter = 20
Angstrom = 21
Mil = 22
Inch = 23
Foot = 24
Mile = 25
Fathom = 26
Unspecified = 100U
Unknown = 101U

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	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 Mailing Lists

If you need more help with a filter, please consider asking your question on the DREAM3D Users mailing list: https://groups.google.com/forum/?hl=en#!forum/dream3d-users