Problem loading tiffs

Hi,

 

I have a problem loading tif-files acquired by an Olympus microscope with the image reader. It produces the error message

'ERROR ReadFileImageTable java.lang.ArithmeticException: / by zero'.

I'm using Knime 2.5.4 on OS X (10.6.8) with KNIP 0.8.0.201204101132 installed. Our diploma student installed the latest versions (??, sorry) on Windows Vista end experiences the same problem. Is this a problem of the tif files (acquired by an Olympus IX81 microscope, see also atatched file within example/data/...)? Converting to png helps, but we have thousands of images and don't want to convert them all in order to be readable in KNIME. Is there an other solution?

 

Thanks and regards

 

Manuel

Hi Manuel,

we know about this problem and therefore we introduced the node "IJ Image Reader (2D) - experimental".

Why the Image Reader is not working:
In the background of the Image Reader we actually just use BioFormats (http://loci.wisc.edu/software/bio-formats). I already sent the link to your example.zip to Melissa from BioFormats and she will take care about this issue. I will keep you informed,...

Until then just use the above mentoined "IJ Image Reader (2D) - experimental", this one should be working. If you have any other questions, don't hesitate to ask :)

Best regards,
Christian

Hi again,

Just got a response from BioFormats: This seems to be a bigger problem ... or in her words "not quite a 5min fix", but they will have it working in the next stable release of bioformats (... which is in a couple of weeks).

http://trac.openmicroscopy.org/ome/ticket/8730

Well anyway, I hope it's working with the "IJ1 Image Reader". If you face any problems, let us know, we will figure something out then. ;)

greetings,

Christian

Hi Christian,

 

many thanks for your reply! Using the "IJ Image Reader (2D) - experimental"-node worked out fine for me. Glad to hear the people at BioFormats are working on this, for me everything is very usable now. 

 

Keep up the good work, best regards

 

Manuel

Hi Manuel,

Melissa fixed the bug. It's in the current trunk, but as it worked out with the IJ2 reader for you, I will wait for the stable BioFormats release to integrate it into KNIME.

One question, just as I am curious: Are you already using the "stable" or the nightly built?
Nightly built has much more functionality, but you may have to reconfigure or reexecute your workflow once in a while.

We plan a 1.0 in the next months ... :)

Grüße,
Christian

Hey Christian,

thanks again for the help, I'll stick to what works now and upgrade later.

At the moment I use the nightly builds. Since I still fiddle around at every corner within the workflows, reconfiguration and reexecution is happening all the time :)

 

Good luck with your 1.0 release,

 

best

 

Manuel