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Import Fiji Montage

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)

The configuration above would result in a data structure as shown in the following image:

Images/ItkImportFijiConfigFile.png

Parameters

Name Type Comment
Input Fiji Tile Configuration File String
Name of Created Montage String Used for the montage infrastructure
Montage Column Start/End Int x 2 The starting and ending column (inclusive) that will be imported
Montage Row Start/End Int x 2 The starting and ending column (inclusive) that will be imported
Length Unit Int Selected from predefined list. See table below
Change Origin Bool = OFF Set the origin of the mosaic to a user defined value
Origin Float 3 Vect 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 Float 3 Vect The luminosity values for the conversion
Cell Attribute Matrix Name String The name of the Cell Attribute Matrix.
Image Data Array Name String The name of the import image data

Color To Gray Scale Notes

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

Required DataContainers

NONE

Required Objects

NONE

Created Objects

This filter will create one data container for each image tile that is in the xml file. That created Data Container will have a Cell Attribute Matrix which will also hold a single Attribute Array of the same type of the image (unless the user selects to convert images to Gray Scale images.)

Kind Default Name Type Component Dimensions Description
Data Container Data Container Name N/A N/A
ImageGeometry N/A N/A
Cell AttributeMatrix N/A N/A
Image Data N/A N/A

Authors:

Contact Info dream3d@bluequartz.net

Version 1.0.0

License See the License.txt file that came with DREAM3D.

Example Pipelines

Prebuilt Pipelines / Examples / ITKImageProcessing / Fiji Import

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