[OpenSPIM] ome-tiff output

[Christoph Sommer]

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". 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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