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Import AxioVision V4 Montage

Group (Subgroup)

Import/Export (Import)

Description

This filter imports in a set of tiled images collected by a Zeiss montaging microscope. The user must point to the XML file which contains the meta-data for all the images. The images must be located in the same directory as the XML file. Each image will be put into an individual Data Container / Attribute Matrix / Attribute Array. The XML input file is the type of file that is put out by the Zeiss Zen software as the "*_info.xml" file and has output that is similar to the following:

  <?xml version="1.0" encoding="utf-8" ?>
  <ROOT>
    <Tags>
        <__Version>536875008<!--__Version-->
        <Count>140</Count>
        <V0>Image</V0>
        <I0>1546</I0>
        <A0>0</A0>
        <V1/>
        <I1>530</I1>
        <A1>0</A1>
        <V2/>
        <I2>1549</I2>
        <A2>0</A2>
        <V3/>
        <I3>1550</I3>
        <A3>0</A3>
        <V4/>
        <I4>1551</I4>
        <A4>0</A4>
        <V5>SampleMosaic.bmp</V5>
        <I5>1553</I5>

The generated data containers will have the pattern of "Prefix_rXXcXX" where the XX is a possibly padded integer indicating either the row or column index that the data container belongs.

Utilizes the itkReadImage and ColorToGrayScale filters

Parameters

Name Type Comment
Input File Path This is the XML file generated by Zeiss that contains information about all of the tiled images
Change Origin Bool Set the origin of the mosaic to a user defined value
Change Spacing Bool Set the spacing of the mosaic to a user defined value
Origin Float 3 Vect The new origin of the mosaic
Spacing Float 3 Vect The new spacing 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
Data Container Prefix The prefix for each created Data Container object
Cell AttributeMatrix Name This attribute matrix holds a single image imported from disk Will be the same for all tiles
Image AttributeArray Name The name of the Attribute Array that holds the image data. Will be the same for all tiles
Meta Data AttributeMatrix Name The name of the Meta-Data AttributeMatrix from the AxioVision _meta.xml file

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.

Required Geometry

Not Applicable

Required Objects

Not Applicable

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

Example Pipelines

Prebuilt Pipelines / Examples / ITKImageProcessing / AxioVision V4 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