icaoberg / Using Bio-Formats command line tools to validate OME-TIFF images

Created Sat, 10 Dec 2016 13:46:38 -0500 Modified Sat, 16 May 2026 15:39:26 -0400
Using Bio-Formats command line tools to validate OME-TIFF images
382 Words
bioformats ome-tiff cellorganizer omero microscopy

CellOrganizer can now save synthetic images as OME-TIFF. The header in an OME-TIFF file is an XML snippet that follows the OME data model.

To generate OME-TIFF files in CellOrganizer, make sure the correct output flag is set:

options.output.OMETIFF = true;

demo3D34

Screenshot

In CellOrganizer, demo3D34 synthesizes an image and saves it as an OME-TIFF.

To validate the OME-TIFF we use the Bio-Formats command line tools, specifically

  • xmlvalid — a command-line XML validation tool that checks an OME-XML document for compliance with the OME-XML schema.

This tool validates the XML snippet in the header against the OME data model schema. The XML header for this example is:

<?xml version="1.0" encoding="utf-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.4" UUID="urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" PhysicalSizeX="0.049" PhysicalSizeXUnit="µm" PhysicalSizeY="0.049" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.2" PhysicalSizeZUnit="µm" SizeC="3" SizeT="1" SizeX="696" SizeY="563" SizeZ="10" Type="uint8"><Channel ID="Channel:0:0" Name="cell" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" Name="nucleus" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" Name="vesicle1" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="5" IFD="5" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="6" IFD="6" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="7" IFD="7" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="8" IFD="8" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="9" IFD="9" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="5" IFD="15" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="6" IFD="16" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="7" IFD="17" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="8" IFD="18" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="9" IFD="19" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="5" IFD="25" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="6" IFD="26" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="7" IFD="27" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="8" IFD="28" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="9" IFD="29" PlaneCount="1"><UUID FileName="cell1.ome.tif">urn:uuid:49279097-4296-40f5-920b-aa60b3c3850c</UUID></TiffData></Pixels></Image></OME>

Running xmlvalid against the OME-TIFF file:

./xmlvalid cell1.ome.tif
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd
Validating cell1.ome.tif
No validation errors found.