Bug 1109 – Grid/Collection stitching not reading Prairie/Bruker stage location metadata

Bug 1109 - Grid/Collection stitching not reading Prairie/Bruker stage location metadata


Summary:	Grid/Collection stitching not reading Prairie/Bruker stage location metadata

Status:	NEEDSINFO

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P5 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2015-07-07 10:21 CDT by Jimmy
Modified:	2015-07-07 15:14 CDT
CC List:	1 user (show)

See Also:

Attachments
Sample Bruker Montage data set (2.92 MB, application/zip) 2015-07-07 10:21 CDT, Jimmy

Description Jimmy 2015-07-07 10:21:12 CDT

Created attachment 253
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

Comment 1 Curtis Rueden 2015-07-07 15:12:13 CDT

Thanks for the report, Jimmy.

It would be good to isolate this behavior to Bio-Formats, by removing ImageJ from the picture. You can use the showinf command line tool of Bio-Formats, with the -omexml option, to dump the resultant OME-XML from the Bruker files. If the stage positions are shown as 0.0 in the XML metadata, then it's a Bio-Formats issue. And in that case, the problem should be reported to the OME team:

https://www.openmicroscopy.org/site/support/bio-formats5.1/about/bug-reporting.html

Comment 2 Curtis Rueden 2015-07-07 15:14:18 CDT

As an aside: I'm sure the Bio-Formats team would appreciate very much if you submitted a patch with your bug report, since my understanding from some internal communication at LOCI here is that this problem might be the result of the new atlas imaging logic?

I say this speaking as the author and de facto maintainer of the Bio-Formats PrairieReader which handles this file format -- the chances are extremely low that I will have the bandwidth to personally address this issue before October.