[ImageJ-bugs] [Bug 1109] New: Grid/Collection stitching not reading Prairie/Bruker stage location metadata

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1109

            Bug ID: 1109
           Summary: Grid/Collection stitching not reading Prairie/Bruker
                    stage location metadata
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P5
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: thex1000 at gmail.com

Created attachment 253
  --> http://fiji.sc/bugzilla/attachment.cgi?id=253&action=edit
Sample Bruker Montage data set

See attached sample Bruker data set.

1. In Fiji:  Plugins-> Stitching -> Grid/Collection Stitching
2. Type:  Positions from file.  Order: Defined by image metadata.
3. Unzip data set.  

Settings for Grid Stitching
Multi series file:  Choose AtlasVolume-07072015-0914-008.xml
Invert X coordinates checked
Invert Y coordinates unchecked
Compute overlap unchecked.  This forces the plugin to read in coordinates.

4.  Click OK.

In the log window, the positions are read in as 0.0 instead of the actual stage
locations and the resulting stitched image is incorrect.  


Other settings that do not matter as much:
Fusion method: linear Blending
Regression th: 0.3
Max/avg displacement th: 2.50
Absolute displacement th: 3.50
Add tiles as ROIs unchecked
Ignore calibration unchecked
Invert z stage position unchecked
subpixel accuracy checked
downsample tiles unchecked
display fusion unchecked
use virtual images unchecked
computation parameters: save memory
image output: fuse and display

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