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<p style="margin: 0px; font-size: 12px; line-height: normal; font-family: Helvetica; color: rgb(69, 69, 69);">
Hi,</p>
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Thank you for sharing your issue and the code as well.</p>
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<p style="margin: 0px; font-size: 12px; line-height: normal; font-family: Helvetica; color: rgb(69, 69, 69);">
You have definitely populated the ome-xml appropriately in your code and Bio-Formats does not currently support the inclusion of channel names in the slice labels, of the ImagePlus object. </p>
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We have filed a ticket to populate the slice labels of the ImagePlus object appropriately,</p>
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https://trac.openmicroscopy.org/ome/ticket/13306</p>
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and you have been added to the cc list. You will be notified when there is a status change on this ticket.</p>
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<p style="margin: 0px; font-size: 12px; line-height: normal; font-family: Helvetica; color: rgb(69, 69, 69);">
As a workaround you could use the following method to populate the global-metadata with an hashmap as follows,</p>
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add<b>GlobalMetaList</b>(“Slice 1:”, ChannelName1);</p>
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add<b>GlobalMetaList</b>(“Slice 2:”, ChannelName1);</p>
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add<b>GlobalMetaList</b>(“Slice 3:”, ChannelName1);</p>
<p style="margin: 0px; font-size: 12px; line-height: normal; font-family: Helvetica; color: rgb(69, 69, 69);">
add<b>GlobalMetaList</b>(“Slice 4:”, ChannelName1);</p>
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This will be populate the original-metadata table with the hash-map as shown above and will thus be available, when you open the image using the ImageJ importer,</p>
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<p style="margin: 0px; font-size: 12px; line-height: normal; font-family: Helvetica; color: rgb(69, 69, 69);">
This is definitely not an ideal solution but can be used as a workaround for the time being(if need be).</p>
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Hope that helps.</p>
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<p style="margin: 0px; font-size: 12px; line-height: normal; font-family: Helvetica; color: rgb(69, 69, 69);">
Best,</p>
<p style="margin: 0px; font-size: 12px; line-height: normal; font-family: Helvetica; color: rgb(69, 69, 69);">
Balaji</p>
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<div style="color: rgb(40, 40, 40);"><span style="background-color: rgb(255, 255, 255);">__________________</span></div>
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<p style="margin-top: 0px; margin-bottom: 0px;">Mr Balaji Ramalingam</p>
<p style="margin-top: 0px; margin-bottom: 0px;">Software Developer<br>
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<p style="margin-top: 0px; margin-bottom: 0px;">OME Team</p>
<p style="margin-top: 0px; margin-bottom: 0px;">School of Life Sciences</p>
<p style="margin-top: 0px; margin-bottom: 0px;">University of Dundee</p>
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<span style="font-weight:bold">From: </span>ome-devel <<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk">ome-devel-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Michael Ellis <<a href="mailto:michael.ellis@dsuk.biz">michael.ellis@dsuk.biz</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 13 October 2016 at 11:08<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-devel] Channel Plane Names Set but not Recognised in ImageJ/BioFormats Plugin<br>
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Dear ome-devel list.
<div class=""><br class="">
</div>
<div class="">I am trying to use the bioformats_package.jar in my Java app to save a single image file comprising multiple channels (each channel acquired with a different fluorescence filter set). I am using the setChannelName() and this appears to work insofar
as I can see the entry being created in the resulting OME-XML data contained within the the .ome.tif file. However, if I use ImageJ with the BioFormats importer plugin, the multi channel image is loaded and displayed, but the channel names are set not to the
names I specify, but “c1/4”, “c:2/4”, “c3/4”, “c:4/4”.</div>
<div class=""><br class="">
</div>
<div class="">My SSCCE is as follows:</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">public class BioFormatsTest2 {</div>
<div class=""><br class="">
</div>
<div class=""> private IMetadata createMetadata(int width, int height, int pixelType, String[] channelNames, Color[] channelColors) {</div>
<div class=""> IMetadata meta;</div>
<div class=""> try {</div>
<div class=""> // create the OME-XML metadata storage object</div>
<div class=""> ServiceFactory factory = new ServiceFactory();</div>
<div class=""> OMEXMLService service = factory.getInstance(OMEXMLService.class);</div>
<div class=""> meta = service.createOMEXMLMetadata();</div>
<div class=""> meta.createRoot();</div>
<div class=""><br class="">
</div>
<div class=""> // define each stack of images - this defines a single stack of images</div>
<div class=""> meta.setImageID("Image:0", 0);</div>
<div class=""> meta.setPixelsID("Pixels:0", 0);</div>
<div class=""><br class="">
</div>
<div class=""> // specify that the pixel data is stored in big-endian format</div>
<div class=""> // change 'TRUE' to 'FALSE' to specify little-endian format</div>
<div class=""> meta.setPixelsBinDataBigEndian(Boolean.TRUE, 0, 0);</div>
<div class=""><br class="">
</div>
<div class=""> // specify that the images are stored in ZCT order</div>
<div class=""> meta.setPixelsDimensionOrder(DimensionOrder.XYCZT, 0);</div>
<div class=""><br class="">
</div>
<div class=""> // specify that the pixel type of the images</div>
<div class=""> meta.setPixelsType(</div>
<div class=""> PixelType.fromString(FormatTools.getPixelTypeString(pixelType)), 0);</div>
<div class=""><br class="">
</div>
<div class=""> // specify the dimensions of the images</div>
<div class=""> meta.setPixelsSizeX(new PositiveInteger(width), 0);</div>
<div class=""> meta.setPixelsSizeY(new PositiveInteger(height), 0);</div>
<div class=""> meta.setPixelsSizeZ(new PositiveInteger(1), 0);</div>
<div class=""> meta.setPixelsSizeC(new PositiveInteger(channelNames.length), 0);</div>
<div class=""> meta.setPixelsSizeT(new PositiveInteger(1), 0);</div>
<div class=""><br class="">
</div>
<div class=""> for (int channel = 0; channel < channelNames.length; channel++) {</div>
<div class=""> meta.setChannelID("Channel:0:" + channel, 0, channel);</div>
<div class=""> meta.setChannelSamplesPerPixel(new PositiveInteger(1), 0, channel);</div>
<div class=""> meta.setChannelName(channelNames[channel], 0, channel);</div>
<div class=""> ome.xml.model.primitives.Color c = new ome.xml.model.primitives.Color(channelColors[channel].getRGB());</div>
<div class=""> meta.setChannelColor(c, 0, channel);</div>
<div class=""> }</div>
<div class=""> } catch (DependencyException | ServiceException | EnumerationException e) {</div>
<div class=""> System.err.println("Failed to populate OME-XML metadata object.");</div>
<div class=""> e.printStackTrace();</div>
<div class=""> meta = null;</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""> return meta;</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""> public static void main(String[] args) throws Exception {</div>
<div class=""> BioFormatsTest2 exporter = new BioFormatsTest2();</div>
<div class=""> exporter.run();</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""> public void run() throws IOException, FormatException {</div>
<div class=""> int width = 256, height = 256;</div>
<div class=""> int pixelType = FormatTools.UINT8;</div>
<div class=""> String[] channelNames = {"Dapi", "Fitc", "TxRed", "Aqua"};</div>
<div class=""> Color[] channelColors = {Color.BLUE, Color.GREEN, Color.RED, Color.CYAN};</div>
<div class=""> String filePath = "/Users/michaelellis/Documents/Development/SmartCapture4/BioFormat2.ome.tif";</div>
<div class=""><br class="">
</div>
<div class=""> // Create image data buffer;</div>
<div class=""> byte[] img = new byte[width * height * FormatTools.getBytesPerPixel(pixelType)];</div>
<div class=""><br class="">
</div>
<div class=""> try (ImageWriter writer = new ImageWriter()) {</div>
<div class=""> IMetadata omexml = createMetadata(width, height, pixelType, channelNames, channelColors);</div>
<div class=""> writer.setMetadataRetrieve(omexml);</div>
<div class=""> writer.setId(filePath);</div>
<div class=""><br class="">
</div>
<div class=""> // only save a plane if the file writer was initialized successfully</div>
<div class=""> for (int planeIndex = 0; planeIndex < channelNames.length; ++planeIndex) {</div>
<div class=""> // savePlane(planeIndex, width, height, pixelType);</div>
<div class=""> // byte[] plane = createImage(width, height, pixelType);</div>
<div class=""><br class="">
</div>
<div class=""> // fill it with random data</div>
<div class=""> for (int i = 0; i < img.length; i++) {</div>
<div class=""> img[i] = (byte) (256 * Math.random());</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""> writer.saveBytes(planeIndex, img);</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""> } // Autoclose writer</div>
<div class=""><br class="">
</div>
<div class=""> }</div>
<div class="">}</div>
</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">The OME-XML in the .ome.tif file is as follows. Note that channel names appear to be Dapi, Fitc, TxRed and Aqua</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""> <OME UUID="urn:uuid:42b524fd-b842-4052-bf6c-5977c9d06a97" xmlns="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a>" xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance" class="">http://www.w3.org/2001/XMLSchema-instance</a>"
xsi:schemaLocation="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a><a href="http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd</a>"></div>
<div class=""> <Image ID="Image:0"></div>
<div class=""> <Pixels BigEndian="true" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="4" SizeT="1" SizeX="256" SizeY="256" SizeZ="1" Type="uint8"></div>
<div class=""> <Channel Color="-16776961" ID="Channel:0:0" Name="Dapi" SamplesPerPixel="1"></div>
<div class=""> <LightPath/></div>
<div class=""> <Channel Color="-16711936" ID="Channel:0:1" Name="Fitc" SamplesPerPixel="1"></div>
<div class=""> <LightPath/></div>
<div class=""> <Channel Color="-65536" ID="Channel:0:2" Name="TxRed" SamplesPerPixel="1"></div>
<div class=""> <LightPath/></div>
<div class=""> <Channel Color="-16711681" ID="Channel:0:3" Name="Aqua" SamplesPerPixel="1"></div>
<div class=""> <LightPath/></div>
<div class=""> <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"></div>
<div class=""> <UUID FileName="BioFormat2.ome.tif">urn:uuid:42b524fd-b842-4052-bf6c-5977c9d06a97</UUID></div>
<div class=""> <TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"></div>
<div class=""> <UUID FileName="BioFormat2.ome.tif">urn:uuid:42b524fd-b842-4052-bf6c-5977c9d06a97</UUID></div>
<div class=""> <TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"></div>
<div class=""> <UUID FileName="BioFormat2.ome.tif">urn:uuid:42b524fd-b842-4052-bf6c-5977c9d06a97</UUID></div>
<div class=""> <TiffData FirstC="3" FirstT="0" FirstZ="0" IFD="3" PlaneCount="1"></div>
<div class=""> <UUID FileName="BioFormat2.ome.tif">urn:uuid:42b524fd-b842-4052-bf6c-5977c9d06a97</UUID></div>
<div class=""> </div>
</div>
<div class=""><br class="">
</div>
<div class="">After loading the created image with the BioFormats Import plugin into Fiji and running the following script:</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""> IJ.log("nSlices=" + nSlices);</div>
<div class=""><br class="">
</div>
<div class=""> for(i = 1; i <= nSlices; i=i+1) {</div>
<div class=""> setSlice(i);</div>
<div class=""> name = getInfo("slice.label");</div>
<div class=""> IJ.log("Slice " + i + ": " + name);</div>
<div class=""> }</div>
</div>
<div class=""><br class="">
</div>
<div class="">The log output is: </div>
<div class=""><br class="">
</div>
<div class="">
<div class=""> nSlices=4</div>
<div class=""> Slice 1: c:1/4</div>
<div class=""> Slice 2: c:2/4</div>
<div class=""> Slice 3: c:3/4</div>
<div class=""> Slice 4: c:4/4</div>
</div>
<div class=""><br class="">
</div>
<div class="">Also, consistent with the script output, the names displayed in the Fiji image window title show the plane names as “c1/4”, “c:2/4”, “c3/4”, “c:4/4”.</div>
<div class=""><br class="">
</div>
<div class="">What am I doing wrong?</div>
<div class="">Am I doing something wrong?</div>
<div class=""><br class="">
</div>
<div class="">Also, I have read the developer documentation at <a href="http://www.openmicroscopy.org/site/support/bio-formats5.2/developers/index.html" class="">http://www.openmicroscopy.org/site/support/bio-formats5.2/developers/index.html</a> but either
I am missing something or there is insufficient explanation for some of the items. For instance in the example <a href="http://www.openmicroscopy.org/site/support/bio-formats5.2/_downloads/FileExport.java" class="">http://www.openmicroscopy.org/site/support/bio-formats5.2/_downloads/FileExport.java</a>,
where can I find an explanation for the string identifiers used in the following calls:</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>meta.setImageID("Image:0", 0);<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>meta.setPixelsID(“Pixels:0", 0);<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>meta.setChannelID(“Channel:0:0", 0, 0);</div>
<div class=""><br class="">
</div>
<div class="">Any help gratefully appreciated!</div>
<div class=""><br class="">
</div>
<div class="">— Michael Ellis</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<pre style="word-wrap: break-word;" class=""><br class=""></pre>
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<div class="">
<div style="text-align: right;" class="">Michael Ellis (Managing Director)</div>
<div style="text-align: right;" class="">Digital Scientific UK Ltd.</div>
<div style="text-align: right;" class=""><a href="http://www.dsuk.biz" class="">http://www.dsuk.biz</a></div>
<div style="text-align: right;" class=""><a href="mailto:michael.ellis@dsuk.biz" class="">michael.ellis@dsuk.biz</a></div>
<div style="text-align: right;" class="">tel: +44(0)1223 911215</div>
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