Filters within OME-XML

The filter model has changed with the June 2007 release of the OME Schema. This page proved a description of the new structures used. The new structures are designed to work for Fluorescence Microscopy but are flexible enough it can also work with filter configurations for most other forms of microscopy. If you feel it will not work in your case than please submit a ticket and we will look into the issue.

Supported Objects

In the schema there is support for the following objects:

Dichroic
The dichroic mirror or dichromatic beamsplitter.
Filter
This object is used to represent any type of excitation filter and emission/barrier filter. It contains details of the transmittance of the filter.
FilterSet
A FilterSet belongs to an Instrument in an OME-XML file and has alongside it any Filters and Dichorics it refers to. It is designed to represent a filter combination, sometimes called a filter cube or filter block. It may contains one excitation filter, one dichroic and one emission filter. Filters and dichroics can be reused across multiple filter sets. It will be normal to have a single dichroic that is usable with several filter combinations.
FilterSetRef
These are used to attach a specific filter set from an Instrument to a LogicalChannel within an Image. They allow the filter set to be defined once in the instrument in an OME-XML file and then used multiple times within the images.
FilterSpec
The filter spec is used by both Dichroic and Filter to store the Manufacturer, Model and LotNumber of the optical element.
FilterWheel
This is a value within a Filter used to record what holder the filter is located in. Although it is named after a wheel it could just as easily be a filter slider or other mechanism. These holders allow any of there containing filters to be automatically selected by the microscope control software.
SecondaryEmissionFilter
This is a value within a LogicalChannel that allows an extra filter to be recorded as placed over the emission filter defined in the FilterSet.
SecondaryExcitationFilter
This is a value within a LogicalChannel that allows an extra filter to be recorded as placed over the excitation filter defined in the FilterSet.

Overview of where the Filter Set sits in the light path

source:/Documentation/Graphics/FilterAndFilterSet/FilterSet-Overview.png

  1. The source produces a beam of light
  2. A small range of wavelength are passed through the Excitation Filter
  3. The light is selectively reflected by the Dichroic mirror to illuminate the sample.
  4. The fluorophore in the sample absorbs the light from 3 and re-emits it on a new wavelength. Some of this re-emitted light travels towards the dichroic mirror.
  5. The light on the new wavelength is selectively transmitted by the dichroic mirror.
  6. The wavelength of detected light is further narrowed and stray reflections reduced by the Emission filter.

Structure of the filter data in OME-XML

The filter data elements are part part of the central OME Schema. The filters are part of the Instrument block. Each instrument can contain zero or more filters, dichroics, and filter sets. Each filter set used unique IDs to referrer to the filters and dichroic it contains. If there are any secondary filters used with the LogicalChannels within an image then those filters are also defines at the instrument level and referenced from the channel using the unique ID. The filters and dichroics are both extensions of the FilterSpec element so store this common data. A filter also contains one TransmittanceRange element that describes the optical characteristic of it.

Diagram showing where FilterSet sits in the OME Schema

source:/Documentation/Graphics/FilterAndFilterSet/FilterSet-Top.png

The FilterSet contains three references, one to a dichroic ID called DichroicRef, and two to filter IDs called ExFilterRef and EmFilterRef. Each of the three references are optional. There is no distinction on whether a filter is designed for emission or excitation at the filter level. The distinction is made within the filter set by the assignment of the filter ID reference to ExFilterRef or EmFilterRef.

The Dichroic object is simple, it simply contains it's unique ID and the values it gets from extending FilterSpec. The FilterSpec values are similar to a the ManufactSpec used elsewhere in that they have Manufacture and Model values. Where there is the difference is in ManufactSpec each object has a serial number where as in FilterSpec the LotNumber of the batch is recorded.

The Filter object has the values it gets by extending FilterSpec and a unique ID the same as the Dichroic. In addition it has a Type and a FilterWheel value. In addition to these extra values it contains one TransmittanceRange object. The TransmittanceRange describes the optical characteristic of the filter and has values for the CutIn and CutOut, along with the CutInTolerance and CutOutTolerance, all expressed in nanometers. There is also the Transmittance of the filter express as a percentage fraction.

Diagram showing the attributes within the filter objects

source:/Documentation/Graphics/FilterAndFilterSet/FilterSet-Links.png

Sample piece of a .ome.xml file showing FilterSet structure

This shows the structure of the resulting xml. It contains dummy data. FilterSet:1 uses Filter:1 for excitation, Filter:2 for Emission, and Dichroic:1. 

<ome:FilterSet ExFilterRef="Filter:1" DichroicRef="Dichroic:1" 
        EmFilterRef="Filter:2" ID="FilterSet:1" 
        Manufacturer="Manufacturer0" Model="Model0" LotNumber="LotNumber0"/>
<ome:Filter Type="LongPass" FilterWheel="FilterWheel0" ID="Filter:1" 
        Manufacturer="Manufacturer10" Model="Model10" LotNumber="LotNumber0">
    <ome:TransmittanceRange CutIn="0" CutOut="0" 
        CutInTolerance="0" CutOutTolerance="0" Transmittance="0"/>
</ome:Filter>
<ome:Filter Type="LongPass" FilterWheel="FilterWheel1" ID="Filter:2" 
        Manufacturer="Manufacturer11" Model="Model11" LotNumber="LotNumber1">
    <ome:TransmittanceRange CutIn="0" CutOut="0" 
        CutInTolerance="0" CutOutTolerance="0" Transmittance="0"/>
</ome:Filter>
<ome:Filter Type="LongPass" FilterWheel="FilterWheel2" ID="Filter:3" 
        Manufacturer="Manufacturer12" Model="Model12" LotNumber="LotNumber2">
    <ome:TransmittanceRange CutIn="0" CutOut="0" 
        CutInTolerance="0" CutOutTolerance="0" Transmittance="0"/>
</ome:Filter>
<ome:Dichroic ID="Dichroic:1" 
        Manufacturer="Manufacturer12" Model="Model12" LotNumber="LotNumber2"/>
<ome:Dichroic ID="Dichroic:2" 
        Manufacturer="Manufacturer18" Model="Model18" LotNumber="LotNumber8"/>