[OpenSPIM] ome-tiff output

[Stephan.Preibisch at mdc-berlin.de]

Hi, did you try using the Autoloader of the MVR/BigStitcher (it’s basically the same now) for import? Activate the BigStitcher update site first to get the newest code. It should handle OME-TIff ... if not, send us a small example and we’ll fix it.

Cheers,
Stephan

Sent from my iPhone

On Nov 7, 2017, at 16:17, Christoph Sommer <christoph.sommer at ist.ac.at<mailto:christoph.sommer at ist.ac.at>> wrote:


Dear HongKee,

thank so much for your recommendation and code. When I understand correctly, it would require the deployment of this VirtualStack class to all ImageJ instances of potential users. I was hoping for a solution, which does not need adaptions of ImageJ.

Alternatively, we could create a different output format in the acquisition (no multi-file OMETiff). I saw that there's already a "IndividualImagesHandler" or an HDF5 handler in "spim.io<http://spim.io>". Does someone have experience with alternative output formats?

Cheers,
Chris


We have also faced those problems because the default image opener is trying to get the metadata for every file.
I really recommend you to make own ImageStack class for reading the metadata just once for your whole series.

We had to create our version of VirtualStack class based on https://imagej.nih.gov/ij/plugins/virtual-opener.html to avoid redundant metadata reading. The below code is not a perfect version, please, use it as a reference.

Hopefully, it will help you.

Cheers,
HongKee

———————————————————

import ij.ImageStack;
import ij.process.ByteProcessor;
import ij.process.ImageProcessor;
import loci.formats.FormatException;
import loci.formats.ImageReader;
import loci.plugins.util.ImageProcessorReader;

import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.FormatException;
import loci.formats.ImageReader;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;

public class MyImageStack extends ImageStack
{
private int bitDepth;
private int width, height;
ImageProcessorReader imageProcessorReader;
private int zSize = 1, tSize = 1, cSize = 1;
private int cEffectiveSize = 1;

public void addSlice( String path )
{
if(path != null)
{
if(width == 0)
{
// create format reader
ImageReader reader = getImageReader( path );

// output dimensional information
int sizeX = reader.getSizeX();
this.width = sizeX;

int sizeY = reader.getSizeY();
this.height = sizeY;

// System.out.println("Effective C" + reader.getEffectiveSizeC());
setcEffectiveSize( reader.getEffectiveSizeC() );

int sizeC = reader.getSizeC();
int sizeZ = reader.getSizeZ();
int sizeT = reader.getSizeT();

// System.out.println( "C=" + sizeC + " Z=" + sizeZ + " T=" + sizeT );

setcSize( sizeC );
setzSize( sizeZ );
settSize( sizeT );

this.bitDepth = reader.getBitsPerPixel();
this.imageProcessorReader = new ImageProcessorReader( reader );
}
}
}

public ImageProcessor getProcessor(int n)
{
// properly implement to get ImageProcessor based on n
}

public static ImageReader getImageReader( String path )
{
ImageReader reader = null;

try
{
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata meta = service.createOMEXMLMetadata();

// create format reader
reader = new ImageReader();
reader.setMetadataStore(meta);

// initialize file
// System.out.println(path);
reader.setId( path );
}
catch ( DependencyException e )
{
e.printStackTrace();
}
catch ( ServiceException e )
{
e.printStackTrace();
}
catch ( IOException e )
{
e.printStackTrace();
}
catch ( FormatException e )
{
e.printStackTrace();
}

return reader;
}
}

———————————————


On Nov 6, 2017, at 10:43 AM, Christoph Sommer <christoph.sommer at ist.ac.at<mailto:christoph.sommer at ist.ac.at>> wrote:

Dear OpenSpim folks,

thanks for creating such a great resource!

We are currently using an OpenSpim setup and the created output is a multi-file ome-tiff. For many applications (e.g. the MVR from Stephan Preibisch et al.) we need to convert the ome-tiff to normal tiff.

Unfortunately, for long time-lapse the conversion takes forever, since for each conversion step all meta-data is parsed from each single time point. My script uses the Bioformats ImporterOptions class, but I can't see how I can bypass the meta-data parsing. I also tried the 'bvconvert' command line script but also got issues there. Also reading from Python (e.g. with the module 'tifffile' only return always the first angle image-stack...)

Would you have any idea?

Cheers,

Chris


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--
HongKee Moon
Scientific Software Engineer
Scientific Computing Facility

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden
Germany

fon: +49 351 210 1923
fax: +49 351 210 1907
www.mpi-cbg.de<http://www.mpi-cbg.de>


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