[ome-users] Loading one series only

[Melissa Linkert]

Hi Thomas,

> I’m using bioformats to read datasets acquired with micromanager (one.tif stacks, split into several files per position when one position is larger than 4gb). Typically, I have 5 positions per experiment (and expect to upscale it up to 20-30); so far I was using this code (imagej macro run using fiji --headless) to open a dataset in a virtual stack:
> 
> > path = "/path/to/file_Pos0.ome.tif";
> > 
> > import ij.*;
> > import loci.plugins.*;
> > import loci.plugins.in.ImporterOptions;
> > ImporterOptions options = new ImporterOptions();
> > options.setId(path);
> > options.setVirtual(true);
> > ImagePlus[] imps = BF.openImagePlus(options);
> > imps[0].show();
> 
> I works well with 5.1 beta (in 5.0 only the first position is loaded successfully). I would like to know if it’s possible to specify to load one series only (in particular to disable the parsing of the metadata of other series, e.g. using options.setSeriesOn() without luck so far). For large dataset, this would make a huge difference in performance in my case (parsing can easily reach on minute per position).

Is this the same problem as discussed a few weeks ago?  See:

http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-March/005145.html

Could you please confirm which of the following you have already tried:

- upgrading to 5.1.0 (released today)
- calling 'options.setUngroupFiles(true);'
- checking the length of 'imps' to verify that the number of ImagePlus
  objects returned

Regards,
-Melissa

On Thu, Apr 02, 2015 at 09:08:02PM +0200, Thomas Julou wrote:
> Hello,
> 
> I’m using bioformats to read datasets acquired with micromanager (one.tif stacks, split into several files per position when one position is larger than 4gb). Typically, I have 5 positions per experiment (and expect to upscale it up to 20-30); so far I was using this code (imagej macro run using fiji --headless) to open a dataset in a virtual stack:
> 
> > path = "/path/to/file_Pos0.ome.tif";
> > 
> > import ij.*;
> > import loci.plugins.*;
> > import loci.plugins.in.ImporterOptions;
> > ImporterOptions options = new ImporterOptions();
> > options.setId(path);
> > options.setVirtual(true);
> > ImagePlus[] imps = BF.openImagePlus(options);
> > imps[0].show();
> 
> I works well with 5.1 beta (in 5.0 only the first position is loaded successfully). I would like to know if it’s possible to specify to load one series only (in particular to disable the parsing of the metadata of other series, e.g. using options.setSeriesOn() without luck so far). For large dataset, this would make a huge difference in performance in my case (parsing can easily reach on minute per position).
> 
> Thank you in advance for your help. Best regards,
> 
> Thomas
> 
> --
> Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
> 

> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users