[ome-users] Reading CZI series image returns empty image while all the metadata are ok

Sebastian Rhode sebrhode at gmail.com
Mon Aug 17 09:13:45 BST 2015


Hi guys,

I recently files a Fiji Bug regarding the BioFormats Importer, but did not
get any response so far. So maybe you are not aware of it yet. The original
bug entry can be found here:

 http://fiji.sc/cgi-bin/bugzilla/show_bug.cgi?id=1139

I attached the 3 screeshos to illustrate the problem.

Sebi



​

​

​

Original Post on Bugzilla:

I downloaded today's version of Fiji and tried to open a CZI series
file via BioFormats 5.1.3 (contains 8 series) as I did many time
before. But when the window opens, where one can select which series
to open, all the thumbnails are black (see screenshot).

The XML metadata see to be OK, but the resulting import image contains
only zeros. This used to work before without any problems and as far
as I remember it wasa even no problem with BF 5.1.3 some days ago...

The CZI image can be found here:
https://dl.dropboxusercontent.com/u/623476/Tiles1_CH%3D2_Z%3D3_T%3D2_B2_B4_SingleCZI.czi
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150817/7416cbfc/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fiji_empty1.png
Type: image/png
Size: 94774 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150817/7416cbfc/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fiji_empty2.png
Type: image/png
Size: 238859 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150817/7416cbfc/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Fiji_empty_ZEN_OK.png
Type: image/png
Size: 761574 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150817/7416cbfc/attachment-0002.png>


More information about the ome-users mailing list