Open Microscopy Environment

Hi

I am writing a fairly simple Jython script to run in headless mode in Fiji and have run into a problem. I have generated an OME-TIFF from some custom code where I have written a polygon ROI into the OME-XML. I want to open the image and display the ROI. I have the following in my script:

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from loci.common import Region
from loci.plugins.in import ImporterOptions
options = ImporterOptions()
options.setShowROIs(True)
options.setColorMode(ImporterOptions.COLOR_MODE_COLORIZED)
options.setId(file)
imps = BF.openImagePlus(options)
for imp in imps:
   imp.show()

But the ROI Manager never opens for the ROI to be selected.

When I try this using the Bioformats Importer it works just fine. I must have missed something!

Cheers,

Dan.

Hi Dan
The showROIs and showOMEXML options are not supported in BF
so nothing wrong with your code: note that you don't need ``from loci.common import Region``, unless you are using it elsewhere
I have opened a Pull Request to address the issue (see https://github.com/openmicroscopy/bioformats/pull/1617)

Thanks for pointing that out.

Cheers
Jmarie

Hi JMarie,

Perhaps I should have checked the source code! Anyway, I made it work by dumping the xml and then getting the ROI from the resultant string.

After parsing I create an ROI and process it:

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from ij.gui import Roi, PolygonRoi

proi = PolygonRoi(xs, ys, len(xs), Roi.POLYGON) 
for i,imp in enumerate(imps):
    print i
    imp.setRoi(proi)
    ip = imp.getProcessor()
    ip.fillOutside(proi)

Then I would like to export the result as OME-TIFF. I tried the easy approach:

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ij.run(imp,"Bio-Formats Exporter", "save=[%s] compression=LZW");

But this gives me:

java.lang.NullPointerException
at net.imagej.patcher.EssentialLegacyHooks.missingSubdirectories(EssentialLegacyHooks.java:164)

I tried using the LociExporter class but I can't seem to make it work without the saveAs GUI popping up. Should I be using the ImageWriter class to do this? Which will require me to "saveBytes" for each plane?

Am I asking this in the right place? Or is this an ImageJ question?

Any advice will be gratefully received!

Cheers,

Dan.

Hi Dan
I had a look at the code and there is no option to save w/o the dialog popping up.
I will push a fix

For the exception you posted it seems to be related to the legacy layer so I assume you are using ImageJ2.
This is more an ImageJ question

Cheers

Jmarie

Hi Jmarie,

Thanks for the feedback. For the record I solved it by using Bioformats as a library in my script:

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writer = ImageWriter()
writer.setMetadataRetrieve(omeMeta)
writer.setId('%s')

# get the stack
planes = imp.getStack()
for p in range(planes.getSize()):

    # get the plane
    plane = planes.getProcessor(p+1)
   
    # fill outside
    plane.fillOutside(proi)
   
    pixels = plane.convertToByte(True).getPixels()
    writer.saveBytes(p,pixels)
   
reader.close()
writer.close()

The reason for this is that I want to run ImageJ (Fiji) for server-side processing. I have a script which:
1. gets Omero ROIs
2 writes them to OME-XML
3 writes the OME-TIFF
4 uses Fiji to process
5 ingests the results of processing using the command line importer

Cheers,

Dan.

Hi Dan

Thanks for the information
Actually, in develop, we have already modified the exporter so you can save the image as ome-tiff w/o dialog popping up.
you will have to specify all the parameters. That could be simplified
Follow some java code we use to generate an ome-tiff of a modified image before import to OMERO.

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StringBuffer buffer = new StringBuffer();
buffer.append("outfile="+f.getAbsolutePath());
buffer.append(" splitz=false");
buffer.append(" splitc=false");
buffer.append(" splitt=false");
buffer.append(" saveroi=true");
buffer.append(" compression="+CompressionType.UNCOMPRESSED.getCompression());
buffer.append(" imageid="+img.getID()+" "); //imageJ image ID
IJ.runPlugIn("loci.plugins.LociExporter", buffer.toString());


The change will be available in the coming 5.1 version.

Cheers

Jmarie