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

[Sebastien Besson (Staff)]

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<mailto: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<mailto: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

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