Open Microscopy Environment

Hello,

We have a microscopy screening pipeline in place. Images are acquired by the microscope, saved in png with metadata, uploaded to a file server and scanned and the metadata dumped into a database. We are studying the possibility of migrating to OME. I have several questions:
1.- I would like to automatically upload files and their metadata to OME. What would be the suggested way of doing this?
2.- We might also migrate to OME-TIFF. Is there any available windows dll to do this?

Regards,

Hernan

If I understand correctly, there are two possible solutions. You can either use OME-TIFF and automatic upload, or you could write directly to the OMERO server API.

For using OME-TIFF, you'll first want to look into bioformats. It's a Java library for reading and writing OME-XML and OME-TIFF. If a DLL is a requirement, you can look into using the new C++ version (feedback welcome!) . Then you'll need to configure OMERO.fs, or more specifically the DropBox, for automatically uploading the OME-TIFFs.

For writing directly to OMERO, you'll need to get either the omero_client.jar or build a omero_client.dll. With those you can connect to the OMERO server directly. For a tutorial on writing an omero client, see http://trac.openmicroscopy.org.uk/omero ... eroClients

Hope that helps,
~Josh

Note: For both solutions, you will need to install the OMERO server

Hello,

Thanks for the quick response. I am trying to write to OME-TIFF. One simple way will be to write a normal tiff with the XML in the description and convert it using ConvertToOmeTiff. However I cannot make the code to work. The error is:

ConvertToOmeTiff.java:7: cannot find symbol
symbol : class BufferedImageReader
location: package loci.formats.gui
import loci.formats.gui.BufferedImageReader;

Any ideas?

Additionally, I would like to write OME-TIFF in Matlab. However, the following simple code does not work.

Code: Select all

im = uint16(repmat( 1:256, 256,1));
writer = loci.formats.out.TiffWriter();
rr = loci.formats.MetadataTools.createOMEXMLMetadata();
rr.createRoot();
imj = im2java2d(im);
writer.setMetadataRetrieve(rr);
writer.setId('test.ome.tif');
writer.saveImage(imj, 1);
writer.close;

loci.formats.FormatException: BigEndian #0 is null
at loci.formats.MetadataTools.verifyMinimumPopulated(MetadataTools.java:317)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:111)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:190)
at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:171)
at loci.formats.FormatWriter.saveImage(FormatWriter.java:130)
at loci.formats.FormatWriter.saveImage(FormatWriter.java:95)

HEG

From loci.formats.MetadataTools:

Code: Select all

  /**
   * Checks whether the given metadata object has the minimum metadata
   * populated to successfully describe the nth Image.
   *
   * @throws FormatException if there is a missing metadata field,
   *   or the metadata object is uninitialized
   */
  public static void verifyMinimumPopulated(MetadataRetrieve src, int n)
    throws FormatException
  {
    if (src == null) {
      throw new FormatException("Metadata object is null; " +
          "call IFormatWriter.setMetadataRetrieve() first");
    }
    MetadataStore store = asStore(src);
    if (store != null && store.getRoot() == null) {
      throw new FormatException("Metadata object has null root; " +
        "call IMetadata.createRoot() first");
    }
    if (src.getPixelsBigEndian(n, 0) == null) {
      throw new FormatException("BigEndian #" + n + " is null");
    }
    if (src.getPixelsDimensionOrder(n, 0) == null) {
      throw new FormatException("DimensionOrder #" + n + " is null");
    }
    if (src.getPixelsPixelType(n, 0) == null) {
      throw new FormatException("PixelType #" + n + " is null");
    }
    if (src.getPixelsSizeC(n, 0) == null) {
      throw new FormatException("SizeC #" + n + " is null");
    }
    if (src.getPixelsSizeT(n, 0) == null) {
      throw new FormatException("SizeT #" + n + " is null");
    }
    if (src.getPixelsSizeX(n, 0) == null) {
      throw new FormatException("SizeX #" + n + " is null");
    }
    if (src.getPixelsSizeY(n, 0) == null) {
      throw new FormatException("SizeY #" + n + " is null");
    }
    if (src.getPixelsSizeZ(n, 0) == null) {
      throw new FormatException("SizeZ #" + n + " is null");
    }
    if (src.getLogicalChannelSamplesPerPixel(n, 0) == null) {
      throw new FormatException("SamplesPerPixel #" + n + " is null");
    }
  }


So, as a minimum you must populate:

• sizeX
• sizeY
• sizeC
• sizeZ
• sizeT
• pixelType
• dimensionOrder
• bigEndian
• samplePerPixel

You can see what this minimum specification looks like here:

http://www.ome-xml.org/wiki/MinimumSpecification

heg wrote:Hello,

One simple way will be to write a normal tiff with the XML in the description and convert it using ConvertToOmeTiff. However I cannot make the code to work. The error is:

ConvertToOmeTiff.java:7: cannot find symbol
symbol : class BufferedImageReader
location: package loci.formats.gui
import loci.formats.gui.BufferedImageReader;

Any ideas?

The ConvertToOmeTiff example that is posted on the LOCI website (http://loci.wisc.edu/ome/ome-tiff-code.html#convert) requires that you use a trunk or daily build of Bio-Formats. I apologize if this was not clear from the website.

heg wrote:
Additionally, I would like to write OME-TIFF in Matlab. However, the following simple code does not work.

Code: Select all

im = uint16(repmat( 1:256, 256,1));
writer = loci.formats.out.TiffWriter();
rr = loci.formats.MetadataTools.createOMEXMLMetadata();
rr.createRoot();
imj = im2java2d(im);
writer.setMetadataRetrieve(rr);
writer.setId('test.ome.tif');
writer.saveImage(imj, 1);
writer.close;

loci.formats.FormatException: BigEndian #0 is null
at loci.formats.MetadataTools.verifyMinimumPopulated(MetadataTools.java:317)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:111)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:190)
at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:171)
at loci.formats.FormatWriter.saveImage(FormatWriter.java:130)
at loci.formats.FormatWriter.saveImage(FormatWriter.java:95)

As Chris mentioned, there is a minimum amount of OME-XML metadata that you must populate. An example of how to populate this metadata is available at:

https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/bio-formats/utils/MinimumWriter.java

Hope that helps,
-Melissa

Thanks for all the support. I have in place a program to write in OME-TIFF. I am now trying to fill all relevant metadata. I have a question related to the Experimenter part (ID, Name, Last Name, etc). Is any of this fields (such as the id) linked to profiles existing in my omero Server installation or this values are completely unrelated?

Regards,

H

heg wrote:Thanks for all the support. I have in place a program to write in OME-TIFF. I am now trying to fill all relevant metadata. I have a question related to the Experimenter part (ID, Name, Last Name, etc). Is any of this fields (such as the id) linked to profiles existing in my omero Server installation or this values are completely unrelated?

Regards,

H

For the obvious security reasons, as far as import is concerned, OMERO ignores experimenter details placed in an OME-TIFF or OME-XML file. All metadata present in an imported OME-TIFF or OME-XML becomes "linked" to the user who initiated the import.

I am having problems to create a properly formatted metadata. I am using the set methods of MetadataStore. As soon as I start to add information about the channels I get the following error message in omero.insight when I try to display the metadata. Afterwards the omero.insight crashes.

omero.UnloadedEntityException: Object unloaded:omero.model.IlluminationI@210563
at omero.model.IlluminationI.errorIfUnloaded(IlluminationI.java:18)
at omero.model.IlluminationI.getValue(IlluminationI.java:124)
at omero.model.Illumination.getValue(Illumination.java:81)
at pojos.ChannelData.getIllumination(ChannelData.java:249)

is there any demo (like MinimumWritter) to write a random multi channel image with full metadata?

Regards,

H

Which version of insight are you using?
Beta 4.0.3?

jmarie

omero.insight 4.0.3
and loci_tools.jar daily build.