Filter and FilterSet 2010-04

This was developed in conjunction with the June 2007 release and updated for the April 2010 release of the OME-XML Model

The filter model has changed with the April 2010 release of the OME Schema. This page provides 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. This is used for the primary dichroic of the instrument. Other Dichroics in the excitation or emission path can be modelled with the Filter object.
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. It can also be used to model a dichroic mirror or dichromatic beamsplitter in the excitation or emission path.
FilterSet:: A FilterSet belongs to an Instrument in an OME-XML file and has alongside it any Filters and Dichroics it refers to. It is designed to represent a collection of filters available on a certain instrument. It can also represent a filter cube or filter block. To represent the set of filters used to collect an image LightPath is a better choice. FilterSet may contain zero or more excitation filters, one dichroic and zero or more emission filters. No ordering of filters is implied. 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 Channel 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.
ManufacturerSpec:: The Manufacturer spec is used by both Dichroic and Filter to store the Manufacturer, Model, SerialNumber 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.
LightPath:: The LightPath object is a child of Channel and is used to represent the collection of Dichroic and Filters used to create the Channel. FilterSet is on an Instrument granularity, LightPath on a Channel of an Image.

Overview of where Filters and Dichroics sit in the optical path

The source produces a beam of light.
A small range of wavelength are passed through the filters in the Excitation path.
The light is selectively reflected by the Dichroic mirror to illuminate the sample.
The fluorphore 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.
The light on the new wavelength is selectively transmitted by the dichroic mirror.
The wavelength of detected light is further narrowed and stray reflections reduced by the filters in the Emission path.
The light can be optionally split by a Dichroic in the emission path to go to two, or more, detectors. This Dichroic is modelled as a Filter of type "Dichroic"
The split light beam can travel directly from the Dichroic to a detector.
The beam may be further filtered before reaching a detector.

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 additional filters used with the Channels within an image then those filters are also defines at the instrument level and referenced from the channel with a LightPath element using the unique ID. The filters and dichroics are both extensions of the ManufacturerSpec 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

The FilterSet contains three kinds of references, one to a dichroic ID called DichroicRef, and two sets to filter IDs called ExcitationFilterRef and EmissionFilterRef. Each of the three kinds 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 (or LightPath) by the assignment of the filter ID reference to either a ExcitationFilterRef or EmissionFilterRef. Not all the objects in a FilterSet need to be used at the same time and there is no ordering implied within the groups of references.

The Dichroic object is simple, it simply contains its unique ID and the values it gets from extending ManufacturerSpec. In ManufacturerSpec each object can have a SerialNumber and/or a LotNumber. The LotNumber is more commonly used in Filters and Dichroics so the batch of manufacture is recorded.

The Filter object has the values it gets by extending ManufacturerSpec 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 where LightPath sits in the OME Schema

The LightPath contains three kinds of references, one to a dichroic ID called DichroicRef, and two sets to filter IDs called ExcitationFilterRef and EmissionFilterRef. Each of the three kinds 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 LightPath by the assignment of the filter ID reference to either an ExcitationFilterRef or EmissionFilterRef. The key difference between LightPath and FilterSet is that ALL the filters in a LightPath have been used and there order is specified.

Diagram showing the attributes within the filter objects

Sample piece of a .ome.xml file showing the Instrument side - the Filter/Dichroic/!FilterSet structure

This shows the structure of the resulting xml.

This defines six filters, five are standard filters, the sixth is a dichroic used as a filter.
It defines two Dichroics that can represent the primary Dichroic in an instrument.
The FilterSet:1 contains Filter:1 and/or Filter:2 for excitation, Dichroic:1 and Filter:3 and/or Filter:4 for Emission.

It contains dummy data.

<ome:FilterSet ID="FilterSet:1" Manufacturer="Ink Inc." Model="Mk 3" LotNumber="K753">
    <ome:ExcitationFilterRef ID="Filter:1"/>
    <ome:ExcitationFilterRef ID="Filter:2"/>
    <ome:DichroicRef ID="Dichroic:1"/>
    <ome:EmissionFilterRef ID="Filter:3"/>
    <ome:EmissionFilterRef ID="Filter:4"/>
</ome:FilterSet>
<ome:Filter ID="Filter:1" Manufacturer="Ink Inc." Model="Medium 490" LotNumber="J23"
    Type="BandPass" FilterWheel="Disk 7">
    <ome:TransmittanceRange Transmittance="0.80" CutIn="450" CutOut="530"/>
</ome:Filter>
<ome:Filter ID="Filter:2" Manufacturer="Ink Inc." Model="Medium 520" LotNumber="J34"
    Type="BandPass" FilterWheel="Disk 7">
    <ome:TransmittanceRange Transmittance="0.75" CutIn="500" CutOut="570"/>
</ome:Filter>
<ome:Filter ID="Filter:3" Manufacturer="Ink Inc." Model="Medium 580" LotNumber="J12"
    Type="BandPass" FilterWheel="Disk 7">
    <ome:TransmittanceRange Transmittance="0.85" CutIn="550" CutOut="620"/>
</ome:Filter>
<ome:Filter ID="Filter:4" Manufacturer="Ink Inc." Model="Medium 630" LotNumber="J09"
    Type="BandPass" FilterWheel="Disk 7">
    <ome:TransmittanceRange Transmittance="0.90" CutIn="590" CutOut="680"/>
</ome:Filter>
<ome:Filter ID="Filter:5" Manufacturer="Ink Inc." Model="Medium 630" LotNumber="J29"
    Type="BandPass" FilterWheel="Disk 7">
    <ome:TransmittanceRange Transmittance="0.60" CutIn="630" CutOut="690"/>
</ome:Filter>
<ome:Filter ID="Filter:6" Model="MirrorBlock Mk II" LotNumber="M538" Type="Dichroic"/>
<ome:Dichroic ID="Dichroic:1" Model="HFT 405/488/543/633"/>
<ome:Dichroic ID="Dichroic:2" Model="MirrorBlock MK II" LotNumber="M539"/>

Sample piece of a .ome.xml file showing the Image side - the LightPath structure