Open Microscopy Environment

I want to stitch Point0000_C0.tiff and Point0000_C1.tiff

When I use:

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bfconvert -version

Version: 5.2.2
VCS revision: 00d095359df2ae798a1ccc6c394347a2f0aebd94
Build date: 12 September 2016

and execute:

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bfconvert -bigtiff -stitch 'Point0000_C<0-1>.tiff' Point0000.tiff

I obtain a correct file with C=2, T=25, Z=1.

However, the same command using:

Version: 5.3.0
Build date: 11 December 2016
VCS revision: 5.3.0

gives me a different file with C=2, T=49, Z=1.

Hi,

Thank you for bringing this to our attention and providing sample data. I was able to test and reproduce the issue as you described. This is certainly a bug and I will log it and begin working on a fix immediately, ensuring testing is in place to prevent any future recurrence.

In the time being, converting to an ome.tiff as below does not appear to display the same symptoms. Alternatively you could continue to use the previous version you have installed until the next bug fix release.
My apologies for any inconvenience caused, hopefully we shall have this resolved shortly.

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bfconvert -bigtiff -stitch 'Point0000_C<0-1>.tiff' Point0000.ome.tiff

David

Thank you for your prompt reply.

The ome.tiff indeed has the correct channel number when I open it with Fiji, however I get the following warning:

Reading IFDs
Populating metadata
Reading IFDs
Populating metadata
[WARN] Error untangling IFDs; the OME-TIFF file may be malformed (IFD #49 missing).

Interestingly, when I open this file with CellProfiler 2.2.0 (rev 9969f42), it cannot resolve metadata for the channel and imports it as a stack of 50 images. I guess, I'll need to bring it to attention of CP guys.

Hi,

many thanks for reporting these warning while opening the exported OME-TIFF. These were effectively cause by a regression in the TIFF writing functionality of Bio-Formats.

We just released Bio-Formats 5.3.1 to address this issue. Please upgrade your command-line tools to use this version and let us know if any issue persists on this front.

Best,
Sebastien