Open Microscopy Environment

Posted: **Mon Nov 24, 2014 12:34 pm**

Hi All

I have written a couple of java classes that use bio-formats to save data as ome-tiff
see https://github.com/imunro/FileWriteSPW.

We are currently trying to integrate these into Micro-Manager (MM) acquisition software.
The problem is that MM uses an old version of bio-formats (sufficiently old to be the old name of scifio.jar).

NB We received the following from the MM team :

"The version in MM is most certainly outdated. As far as I know, there is
no particular reason why we need the old version, but updating it would
certainly require careful checking to make sure nothing breaks. It's use
in Micro-Manager is limited to the writing of OME-XML metadata when
writing the (standard) image stack file format."

We don't really have the bandwidth to update MM to the newer bio-formats and then maintain our own version.

The Java classes in question use a limited number of components from bioformats_package.jar (included below)
Can anyone tell me which components within bioformats_package.jar are required and whether those components will still clash with scifio.jar or ,even better,can anyone suggest an easier solution.

Many thanks

Ian

import loci.common.services.DependencyException;
import loci.common.services.ServiceException;
import loci.common.services.ServiceFactory;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.ImageWriter;
import loci.formats.meta.IMetadata;
import loci.formats.ome.OMEXMLMetadata;
import loci.formats.services.OMEXMLService;
import loci.formats.MetadataTools;
import loci.common.DataTools;

import ome.xml.model.enums.DimensionOrder;
import ome.xml.model.enums.EnumerationException;
import ome.xml.model.enums.PixelType;
import ome.xml.model.primitives.PositiveInteger;
import ome.xml.model.primitives.NonNegativeInteger;
import ome.xml.model.enums.NamingConvention;

Posted: **Tue Nov 25, 2014 4:48 pm**

Hi Ian,

Here's an independent test which works (aka : Uses Bioformats_package (5.0.6) and exports images snapped from Micromanager as ome-tiff).

I have included the acquisition angle as well to cover the complete workflow (and am guessing that you're problem might be more at the acquisition side of things). There are multiple methods to snap images in micromanager, so am just attaching the script that worked for me.

Code: Select all: %Import packages import org.micromanager.MMStudioMainFrame; import org.micromanager.acquisition.AcquisitionWrapperEngine; import ij.*; import ij.io.FileSaver; import org.micromanager.utils.ImageUtils; import ij.process.ImageProcessor; import ij.ImagePlus; import org.micromanager.api.Autofocus; import ij.text.TextCanvas; import org.micromanager.plugin.*; import loci.plugins.out.Exporter; gui = MMStudioMainFrame(false); f = warndlg('Press ok once config file is loaded', 'Note'); gui.show; drawnow;waitfor(f); mmc = gui.getCore; mmc.loadSystemConfiguration ('/Applications/Micro-Manager1.4/MMConfig_demo.cfg'); %parameters exposures = [0,10,100,1000]; config_groups=mmc.getAvailableConfigGroups(); channels=mmc.getAvailableConfigs(config_groups.get(1)); %Image Output Directory and Suffix for Image Name acqRoot = [pwd '/']; AcqName = 'Test_Config'; numFrames = 10; numSlices =1 ; gui.openAcquisition(AcqName, acqRoot, numFrames, length(channels), numSlices); for i=1:channels.size gui.setChannelName(BrightAcqName, i-1, char(channels.get(i-1))); end plugin = loci.plugins.LociExporter(); for i=0:numFrames-1 for j=1:channels.size mmc.setConfig(config_groups.get(1), char(channels.get(j-1))); mmc.setExposure(exposures(j)); mmc.snapImage(); img = mmc.getImage(); % returned as a 1D array of signed integers in row-major order width = mmc.getImageWidth(); height = mmc.getImageHeight(); %Saving image proc0 = ImageUtils.makeProcessor(mmc, img); imgp0 = ImagePlus('',proc0); if i==0 gui.displayImage(img); image = IJ.getImage(); exporter = loci.plugins.out.Exporter(plugin, image); exporter.run(); keyboard end end end

Plus here's my class path,

Which contains both Bioformats_package(5.0.6) and the jars packaged within micromanager.

The above example uses the bioformats_exporter plugin to export images as ome-tiff's. Similarly, your SPWwriter should also not face any conflicts while exporting, if the acquisition side of things are picked properly.

Please let me know if this doesnt makes sense.

Best,
Balaji

Posted: **Tue Nov 25, 2014 4:51 pm**

Thanks for all your efforts Balaji

Ian

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