[ome-users] bfconvert of .r3d file

Wed Mar 9 20:54:54 GMT 2016

Hi Alex,

thanks for the additional information. I tried to reproduce your issue on CentOS 6.7
with one of the r3d files in our data repository. However I was unsuccessful at
reproducing it.  After converting the image using the same command as you
posted  and importing both the original and the converted one into OMERO, pixels
have the same intensities.

Would it be possible for you to upload one of your failing images at
http://qa.openmicroscopy.org.uk/qa/upload/

Best,
Sebastien

On 8 Mar 2016, at 19:13, Alexandre Cunha <cunha at caltech.edu<mailto:cunha at caltech.edu>> wrote:

Hi Melissa,

The output of md5sum is the same for both systems. The tiff validation is nothing special. I did a visual check of a few slices and they are totally off, the .r3d is a FISH image with a few bright spots on a dark background, all float values, and the generated tiff is a saturated bright all over for some slices and a mix of saturated and dark pixels for others. I also checked a few pixel values using "gmic -o -.asc". Though the tiffinfo reporst 32-bit floats on the Redhat system, the actual values seem to be integers at 16-bit quantization, it doesn't make sense. Some unsolicited conversion is being done.

I tried different versions of java, installed an up-to-date libtiff, but the problem persists on the Redhat system - not on Ubuntu. I didn't build bfconvert from source but used bftools.zip to deploy it in both systems. I can't tell for sure if there is something wrong with the Redhat cluster - it is, after all, a possibility - but this is the only application I am aware is behaving oddly.

Let me know if you would like me to send directly to you the .r3d I am using for tests and a few generated tiff slices.

Best,
- Alex

On 03/08/2016 06:32 AM, Melissa Linkert wrote:
Hi Alex,

Thank you for reporting this.

We run bfconvert to convert .r3d files, (Deltavision, 32-bit floats) into tiff slices, as in

    bfconvert -separate file.r3d slice.%c.%z.tiff

for further processing. It works well under Ubuntu 14.04 but it chokes under Red Hat Enterprise Linux Server release 6.7 producing faulty tiff slices (pixel values are incorrect, e.g. all pixels have 65535). In my tests I use bfconvert versions 5.0.2 and 5.1.8 on both systems.

We're trying a few things to duplicate the problem now, but in the
meantime could you please confirm that the output of 'md5sum file.r3d'
is the same on both systems?  It would also be useful to know which
software is being used to validate the converted TIFF files, as that
may help to point us in the right direction.

Regards,
-Melissa

On Mon, Mar 7, 2016 at 7:01 PM, Alexandre Cunha <cunha at caltech.edu<mailto:cunha at caltech.edu>> wrote:

Hi,

We run bfconvert to convert .r3d files, (Deltavision, 32-bit floats) into tiff slices, as in

    bfconvert -separate file.r3d slice.%c.%z.tiff

for further processing. It works well under Ubuntu 14.04 but it chokes under Red Hat Enterprise Linux Server release 6.7 producing faulty tiff slices (pixel values are incorrect, e.g. all pixels have 65535). In my tests I use bfconvert versions 5.0.2 and 5.1.8 on both systems.

I was wondering if this is a known problem on RedHat machines and/or .r3d files. Any advice?

Many thanks,
- Alex

---

[607] : bfconvert -version
Version: 5.1.8
VCS revision: 9eb8da31c1f01989f439963b9cc215b4398bedd8
Build date: 12 February 2016

OR

(bfconvert -version
Version: 5.0.2
VCS revision: 0c4215a
Build date: 27 May 2014)

lsb_release -a

LSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 6.7 (Santiago)
Release:        6.7
Codename:       Santiago

Distributor ID: Ubuntu
Description:    Ubuntu 14.04.4 LTS
Release:        14.04
Codename:       trusty

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