[ome-users] Binned Hamamatsu .cxd file error

[David Gault (Staff)]

Hi Georg,

Thank you for reporting this problem and for providing sample files. I was able to test and reproduce the same issue as you reported with the latest Bio-Formats release.
From debugging the issue it appears to be caused as the number of bytes read per plane is greater than the Bio-Formats reader expects. The reader tries to adjust the image width to account for this. In this scenario it has adjusted it incorrectly, however we have other sample files in our repository which require the adjustment to be made.

If we can better understand these two scenarios for .cxd files then we should be able to make a fix available.
Are you aware if this issue is only present in files when Binning is set or have you noticed it present in other files also?

With Thanks,
David Gault

On 25 Apr 2017, at 02:23, Georg Vogler <gvogler at sbpdiscovery.org<mailto:gvogler at sbpdiscovery.org>> wrote:

Hi!

I have trouble opening movie files created with HCImage using current installations of FIJI or Image with bioformats importer (fully updated).

While regular cxd files import just fine, it seems that files that were recorded with 4x binning don’t open properly but show a distorted image.


Original cxd file: https://www.dropbox.com/s/wppbc8w0xumsbfx/tdGFP%20adult%20heart%20x%20Hand42-Gal4%20%232.cxd?dl=0

How it is displayed (on MacOS and Windows 7 64bit):https://www.dropbox.com/s/7d1egax8zmegpcz/Screen%20Shot%202017-04-24%20at%206.20.48%20PM.png?dl=0


Can you see if this is fixable? I had seen this problem before but I’m not sure if it got resolved since then.

Thanks a lot,

Geo


Georg Vogler, Ph.D.
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Sanford Burnham Prebys Medical Discovery Institute
Development, Aging and Regeneration
Staff Scientist
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