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

[Fethallah Benmansour]

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
>
>
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