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Unable to read Olympus apl database

https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8013

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Unable to read Olympus apl database

PostPosted: Tue Mar 08, 2016 12:56 pm
by klaus
Hello,

I am trying to read an Olympus APL database with Bio-Formats (with Fiji 2.0.0-rc-43/1.50g). It is the example database ("LifeScienceDemoSTAR.apl") that was supplied with our intallation of of the cell^p software from Olympus - later I would want to read "our" database.
The Dataset Structure Table says that I have to open "One .apl file, one .mtb file, one .tnb file, and a directory containing one or more .tif files" and here I encounter my first problem: How do I open multiple files with Bio-Formats? So far I have tried to open them piecewise via the Bio-Formats plugin and via drag and drop of all files onto the Bio-Formats shortcut window. This always leads me to the Bio-Formats Import Options and then, whatever I use as options will result in an exception like the one below. What am I missing? Any info would be welcome!

Thanks a lot,
Klaus

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.50g; Java 1.6.0_24 [32-bit]; Windows 7 6.1; 20MB of 1148MB (1%)

java.lang.IllegalArgumentException: Invalid series: 0
at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1284)
at loci.formats.FormatReader.setSeries(FormatReader.java:970)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:196)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:101)
at loci.formats.in.APLReader.initFile(APLReader.java:428)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:212)
at ij.IJ.runPlugIn(IJ.java:176)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:662)

Re: Unable to read Olympus apl database

PostPosted: Wed Mar 09, 2016 4:20 pm
by mlinkert
Hi Klaus,

Thank you for reporting this problem.

I am trying to read an Olympus APL database with Bio-Formats (with Fiji 2.0.0-rc-43/1.50g). It is the example database ("LifeScienceDemoSTAR.apl") that was supplied with our intallation of of the cell^p software from Olympus - later I would want to read "our" database.
The Dataset Structure Table says that I have to open "One .apl file, one .mtb file, one .tnb file, and a directory containing one or more .tif files" and here I encounter my first problem: How do I open multiple files with Bio-Formats?


You only need to open the .apl file; the dataset structure table doesn't indicate that you need to manually open every file listed, but rather that all of those files are important and shouldn't be removed from the dataset.

So far I have tried to open them piecewise via the Bio-Formats plugin and via drag and drop of all files onto the Bio-Formats shortcut window. This always leads me to the Bio-Formats Import Options and then, whatever I use as options will result in an exception like the one below.


Could you please verify that your Fiji installation is up to date? "Help > About Plugins > Bio-Formats Plugins" should show that the version number is 5.1.8. If you see this error message with 5.1.8, then it would be helpful if you could upload the entire dataset to https://www.openmicroscopy.org/qa2/qa/upload/ so that we can duplicate the problem.

Regards,
-Melissa

Re: Unable to read Olympus apl database

PostPosted: Wed Mar 09, 2016 8:54 pm
by klaus
Dear Melissa,

thank you very much for taking a look at my problem. I verified my version of Bio Formats and it is indeed 5.1.8. So I just uploaded the dataset to your server ("LifeScienceDemo.zip"). It is a demo database from Olympus and might be copyrighted somehow. If you need another dataset I can provide something with pictures from our own microscope.

Greetings,
Klaus

Re: Unable to read Olympus apl database

PostPosted: Fri Mar 11, 2016 5:12 pm
by dgault
Hi Klaus,

Apologies for the delay in responding, I was able to debug into this issue more today. It appears that the problem is due to our APL reader being unable to locate the associated tiff files. This is most likely due to our reader having parsed the database incorrectly. This will require further investigation and a bug fix on our part.

Note: I have edited the above reply after further testing, if you read the original reply there is no need to upload further files at this time

With Thanks,
David

Re: Unable to read Olympus apl database

PostPosted: Wed Mar 16, 2016 5:38 pm
by dgault
Hi Klaus,

I just wanted to provide an update on this issue. Further investigation has shown that this does indeed appear to a bug in the way we are reading the database. I do not yet have a solution but I have created a ticket in order to keep track of this bug - https://trac.openmicroscopy.org/ome/ticket/13174#ticket

With Thanks,
David Gault

Re: Unable to read Olympus apl database

PostPosted: Thu Mar 17, 2016 7:56 am
by klaus
Hi David,

thank you for the update. If necessary I can provide some more data. I could define one ore more small databases with pictures from our microscope. Just let me know.

Greetings,
Klaus

Re: Unable to read Olympus apl database

PostPosted: Thu Mar 17, 2016 7:02 pm
by dgault
Hi Klaus,

Thank you for that offer, if you have additional sample data that would certainly be most helpful. The more file sets we have the easier it is for us to verify and test our readers.

If you have any additional data that could be uploaded to https://www.openmicroscopy.org/qa2/qa/upload/ that would be appreciated.

With Thanks,
David

Re: Unable to read Olympus apl database

PostPosted: Fri Mar 18, 2016 4:48 pm
by klaus
Hi David,

I just uploaded four databases:

    ExampleDatabase.zip: An example from Olympus.
    MaterialsDemo.zip: Another example from Olympus
    plain.zip: A "minimal" database that I created from scratch with a few pictures from our lab. I has no additional metadata fields.
    example2.zip: The same pictures as in plain.zip but with some additional fields (actually I took our "normal" database as a template). The data in these fields is mostly identical for all pictures.

If you need more examples, just ask.

Good luck and a nice weekend,
Klaus

Re: Unable to read Olympus apl database

PostPosted: Tue Mar 22, 2016 10:13 am
by dgault
Hi Klaus,

Just a further update, I have tested the uploaded sample files and discovered a number of issues. I have opened a PR, https://github.com/openmicroscopy/bioformats/pull/2304 which should address most of these and allow the filesets to be opened with Bio-Formats. Once the PR is tested and approved it will be scheduled for an upcoming Bio-Formats release.

There is still one further issue from the ExampleDatabase file, as such I am leaving the ticket http://trac.openmicroscopy.org/ome/ticket/13174 open for the time being.

Thank you again for reporting this issue and for the help in providing sample datasets.

David

Re: Unable to read Olympus apl database

PostPosted: Mon Apr 04, 2016 11:15 am
by klaus
Hi David,

thanks a lot for all the work!
I am not familiar with Bug tracking systems etc. but I think I figured out (from the links in your last post) that you have provided a fix for the apl-reader. Do you have any information when this will be available?

Greetings,
Klaus
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