[ome-users] Z-dimension bug with Andor TIFF

[David Gault (Staff)]

Hi James,

Thank you for following up on this and uploading a sample data set. You are correct that we had added the PhysicalSizeZ along with TheZ=“2”, however the exact Z Position for each image would have to be calculated from these values by the user.
I have opened a PR to address this and populate the PositionZ for each image . You can view the PR below, it should be included in the next Bio-Formats release 5.1.7:
https://github.com/openmicroscopy/bioformats/pull/2117

With regards the ability to copy OME metadata from the FIJI display window, the copy and paste functionality here comes directly from Java. I have tested it myself on Windows and Mac and it appears to be working OK. Its worth noting that when you copy a line it is actually copying an XML element so in some text editors you may need to use Paste and Match Style. Alternatively if you are still having issues copying the metadata it may be due to the JVM not having access to the clipboard, in which case you would need to create a permission rule in your Java policy to give AWTPermission accessClipboard.

Lastly regarding the drag and drop functionality, in Fiji if you simply drag and drop a file, by default Fiji will use built-in handling to open certain image files including some Tiff formats, for other formats it will use the Bio-Formats Importer. To be sure that you are reading files from the Bio-Formats Importer we would recommend accessing it via the Plugins menu.

With Thanks,
David Gault

On 25 Nov 2015, at 10:03, James Wainwright <jimboesq at gmail.com<mailto:jimboesq at gmail.com>> wrote:

I've uploaded a sample dataset using the following link:

https://www.openmicroscopy.org/qa2/qa/upload/

James



On 25 November 2015 at 09:58, James Wainwright <jimboesq at gmail.com<mailto:jimboesq at gmail.com>> wrote:
Hi there,

I don't think this has been fixed?

I've tested in version 5.1.6 and the OME metadata still shows:

PositionZ="0.0"

It does however show:

TheZ="2" for the third Z slice, which is sort of correct, but this must then be translated back to a Z position by the user who would need to look further up in the OME metadata at the following entry:

PhysicalSizeZ

To make matters worse, it doesn't seem possible to copy or paste this OME metadata any more! I can select a line, and use CTRL-A to select all, but cannot paste it (presumably because I cannot copy it).

Finally, I'm convinced that once upon a time, I was able to simply drag a TIFF onto FIJI and it would auto-load Bioformats because it recognised it as a compatible file. Could this feature be enabled again?

Thanks!

James



On 29 September 2015 at 14:58, James Wainwright <jimboesq at gmail.com<mailto:jimboesq at gmail.com>> wrote:
Hi again,

A user has pointed out, and I have confirmed, that the Z dimension is incorrectly sized when opening an Andor TIFF with Bioformats. I guess this is similar to Bug 12964, which I previously reported.

Basically, Bioformats seems to ignore the actual Z-step used and uses the frame number instead - i.e. 1um Z-step for everything.

I've uploaded a dataset created by the latest version of Andor iQ (3.3.2) here:

http://www.andor.com/ftp/8670/Protocol1.zip

The text file should show the correct metadata, namely:

XY (pixels) = 0.696
Z (Z-step) = 0.86

Let me know if it helps or if you need more!

Thanks a lot!

James


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