[ome-users] Issue with Bioformat reading ets/vsi files

[Fethallah Benmansour]

Hi Sebastien,

Yes, that worked.

Thanks a lot to you and to Melissa for the great support.

--
Fethallah

On Thu, Jul 23, 2015 at 10:34 AM, Sebastien Besson (Staff) <
s.besson at dundee.ac.uk> wrote:

>  Hi Fethallah,
>
>  according to the ReaderWrapper.setFlattenedResolutions
> <http://downloads.openmicroscopy.org/bio-formats/5.1.3/api/loci/formats/ReaderWrapper.html#setFlattenedResolutions(boolean)> Javadoc
> [1],
> you may want to try the following on MATLAB:
>
>  >> reader.setFlattenedResolutions(false);
>
>  Best,
> Sebastien
>
>  [1]
> http://downloads.openmicroscopy.org/bio-formats/5.1.3/api/loci/formats/ReaderWrapper.html#setFlattenedResolutions(boolean)
>
>  On 23 Jul 2015, at 09:19, Fethallah Benmansour <
> fethallah.benmansour at gmail.com> wrote:
>
>  Dear Mellissa,
>
>  Thanks for your prompts answer.
>
>  Unfortunately, we're having an error when executing
> reader.setFlattenedResolutions('false');
>  >> No method 'setFlattenedResolutions' with matching signature found for
> class
> 'loci.formats.ChannelSeparator'.
>
>  We double checked that we are using the latest version of bfmatlab
> (and bioformats_package.jar).
>
>  Could you please help ?
>
>  Best,
>
>  --
> Fethallah
>
> On Wed, Jul 22, 2015 at 9:12 PM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
>
>> Hi Fethallah,
>>
>> > From Matlab, we are using the the bioformat toolbox to read vsi files
>> > (cellSens VSI from Olympus).
>> >
>> > The vsi file is pointing to a few frame_t.ets files located in
>> > sub-directories as follows:
>> > --- stack1           : code bar (not interesting for us)
>> > --- stack10000   : low resolution whole  slide image (not interesting
>> for
>> > us)
>> > --- stack10002   : high resolution image of a selected box
>> > --- stack10005   : high res image of an other selected box
>> >
>> > Our problem is that even if we specify to the bfGetReader function to
>> read
>> > the file under stack10005/frame_t.ets, it is reading
>> stack10002/frame_t.ets
>> > instead.
>>
>> The .ets files are always grouped together with the corresponding .vsi
>> file, so this is expected.  Choosing any one of the files from the
>> dataset will initialize the whole dataset when bfGetReader is called.
>>
>> > Is there a way to force it to read a specific stack from the slide ?
>> > From the java code, it seems that when an *.ets file is passed then it
>> > point back to the associated vsi file...
>>
>> The easiest way to do that is something like:
>>
>> %%%
>> reader = bfGetReader(); % do not specify the file name just yet
>> reader.setFlattenedResolutions('false');
>> reader.setId('name_of_file.vsi'); % an .ets file name can also be used
>> here
>>
>> % numberOfStacks should be 5 in the above example
>> % one for each .ets file, and one for the .vsi file
>> numberOfStacks = reader.getSeriesCount();
>>
>> % this should specify 'stack10005'; the .ets files are
>> % in the same order as their respective directory names, and
>> % the .vsi file is last
>> stackIndex = numberOfStacks - 1;
>> reader.setSeries(stackIndex);
>>
>> % now the reader is set to retrieve the correct images
>> % when using bfGetPlane (you may need to modify this call
>> % to retrieve a tile instead of the whole image)
>> image = bfGetPlane(reader, 0);
>> %%%
>>
>> If that doesn't work, please let us know.
>>
>> Regards,
>> -Melissa
>>
>> On Wed, Jul 22, 2015 at 05:28:43PM +0200, Fethallah Benmansour wrote:
>> > Dear Support,
>> >
>> > From Matlab, we are using the the bioformat toolbox to read vsi files
>> > (cellSens VSI from Olympus).
>> >
>> > The vsi file is pointing to a few frame_t.ets files located in
>> > sub-directories as follows:
>> > --- stack1           : code bar (not interesting for us)
>> > --- stack10000   : low resolution whole  slide image (not interesting
>> for
>> > us)
>> > --- stack10002   : high resolution image of a selected box
>> > --- stack10005   : high res image of an other selected box
>> >
>> > Our problem is that even if we specify to the bfGetReader function to
>> read
>> > the file under stack10005/frame_t.ets, it is reading
>> stack10002/frame_t.ets
>> > instead.
>> >
>> > Is there a way to force it to read a specific stack from the slide ?
>> > From the java code, it seems that when an *.ets file is passed then it
>> > point back to the associated vsi file...
>> >
>> > Thank you into advance,
>> >
>> > Kind regards,
>> >
>> > --
>> > Fethallah
>>
>>  > _______________________________________________
>> > ome-users mailing list
>> > ome-users at lists.openmicroscopy.org.uk
>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>  _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150723/4bf3be60/attachment.html>