<?xml version="1.0" encoding="UTF-8"?>
<!-- 
  **********************************************************************
  * FuGEFlow Experiment Annotation Example
  * **************************************
  * 
  * This document represents a Gating-ML file that is part of an
  * example description of a flow cytometry experiment that is compliant 
  * with the Minimum Information about a Flow Cytometry Experiment 
  * (MIFlowCyt).
  * 
  * The purpose of the example is to validate FuGEFlow - a Flow Cytometry
  * specific extension of the FuGE model. Validation is understood in terms of
  * whether the FuGEFlow XML schema defines a language that allows to describe
  * flow cytometry experiments.
  *
  * The example is based on 
  * "MIFlowCyt Experiment Annotation Example" from February 20th, 2008
  * by Maura Gasparetto, Josef Spidlen, and Ryan R. Brinkman
  * 
  * License
  * The work may be used under the terms of the 
  * Creative Commons Attribution-ShareAlike 3.0 Unported license. 
  * You are free to share (copy, distribute and transmit), and adapt 
  * the work under the conditions specified at 
  * http://creativecommons.org/licenses/by-sa/3.0/legalcode
  * 
  * Acknowledgement
  * This work has been supported by NIH grant EB005034 from the 
  * National Institute of Biomedical Imaging And Bioengineering.
  * 
  * Disclaimer
  * The content is solely the responsibility of the authors and 
  * does not necessarily represent the official views of the 
  * National Institute of Biomedical Imaging And Bioengineering 
  * or the National Institutes of Health.
  *
  * Josef Spidlen, Ph.D., jspidlen@bccrc.ca, April 11, 2008
  ************************************************************************ 
-->
<gating:Gating-ML 
  xmlns:gating="http://www.isac-net.org/std/Gating-ML/v1.5/gating"
  xmlns:transformation="http://www.isac-net.org/std/Gating-ML/v1.5/transformations"
  xmlns:data-type="http://www.isac-net.org/std/Gating-ML/v1.5/datatypes"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="
    http://www.isac-net.org/std/Gating-ML/v1.5/gating 
    file:///mnt/e/XML-based_FCM_Standards/Gating-ML.v1.5/XML-schemas/Gating-ML.v1.5.xsd
  ">
  
  <!-- Spillover matrix that defines the compensation -->
  <transformation:spilloverMatrix transformation:id="spillover_01">
    <transformation:parameters>
      <data-type:parameter data-type:name="FL1-A" />
      <data-type:parameter data-type:name="FL2-A" />
      <data-type:parameter data-type:name="FL3-A" />
      <data-type:parameter data-type:name="FL4-A" />
      <data-type:parameter data-type:name="FL5-A" />
      <data-type:parameter data-type:name="FL6-A" />
      <data-type:parameter data-type:name="FL7-A" />
      <data-type:parameter data-type:name="FL8-A" />
    </transformation:parameters>
    <transformation:spillover> <!-- FL1-A -->
      <transformation:coefficient transformation:value="1" />
      <transformation:coefficient transformation:value="0.2" />
      <transformation:coefficient transformation:value="0.04" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
    </transformation:spillover>
    <transformation:spillover> <!-- FL2-A -->
      <transformation:coefficient transformation:value="0.007" />
      <transformation:coefficient transformation:value="1" />
      <transformation:coefficient transformation:value="0.23" />
      <transformation:coefficient transformation:value="0.029" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
    </transformation:spillover>
    <transformation:spillover> <!-- FL3-A -->
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0.18" />
      <transformation:coefficient transformation:value="1" />
      <transformation:coefficient transformation:value="0.25" />
      <transformation:coefficient transformation:value="0.02" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
    </transformation:spillover>
    <transformation:spillover> <!-- FL4-A -->
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="1" />
      <transformation:coefficient transformation:value="0.12" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
    </transformation:spillover>
    <transformation:spillover> <!-- FL5-A -->
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0.25" />
      <transformation:coefficient transformation:value="0.05" />
      <transformation:coefficient transformation:value="0.008" />
      <transformation:coefficient transformation:value="1" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
    </transformation:spillover>
    <transformation:spillover> <!-- FL6-A -->
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0.03" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="1" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
    </transformation:spillover>
    <transformation:spillover> <!-- FL7-A -->
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="1" />
      <transformation:coefficient transformation:value="0" />
    </transformation:spillover>
    <transformation:spillover> <!-- FL8-A -->
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="0" />
      <transformation:coefficient transformation:value="1" />
    </transformation:spillover>
  </transformation:spilloverMatrix>
  
  <!-- The initial FSC/SSC gate defining leukocytes -->
  <gating:PolygonGate gating:id="Leukocytes">
    <gating:dimension><data-type:parameter data-type:name="FSC-A" /></gating:dimension>
    <gating:dimension><data-type:parameter data-type:name="SSC-A" /></gating:dimension>
    <gating:vertex>
      <gating:coordinate data-type:value="1125" />
      <gating:coordinate data-type:value="200" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="1750" />
      <gating:coordinate data-type:value="550" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="2200" />
      <gating:coordinate data-type:value="625" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="3200" />
      <gating:coordinate data-type:value="2250" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="3500" />
      <gating:coordinate data-type:value="3250" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="3450" />
      <gating:coordinate data-type:value="3500" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="2750" />
      <gating:coordinate data-type:value="3780" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="2250" />
      <gating:coordinate data-type:value="3900" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="2000" />
      <gating:coordinate data-type:value="3500" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="1300" />
      <gating:coordinate data-type:value="1300" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="900" />
      <gating:coordinate data-type:value="300" />
    </gating:vertex>
  </gating:PolygonGate>
  
  <!-- The FSC/FL8(DAPI) gate defining viable leukocytes -->
  <gating:RectangleGate 
    gating:id="Viable_Leukocytes" 
    gating:parent_id="Leukocytes">
    <gating:dimension gating:min="900" gating:max="3260">
      <data-type:parameter data-type:name="FSC-A" />
    </gating:dimension>
    <gating:dimension gating:max="1200">
      <data-type:parameter data-type:name="FL8-A" />
    </gating:dimension>
  </gating:RectangleGate>
  
  <!-- The FL1(CD45.1)/FL4(CD45.2) gate defining donor-derived viable leukocytes -->
  <gating:RectangleGate 
    gating:id="Donor-derived_Viable_Leukocytes" 
    gating:parent_id="Viable_Leukocytes">
    <gating:dimension gating:min="2200" gating:max="100000">
      <data-type:parameter data-type:name="FL1-A" />
    </gating:dimension>
    <gating:dimension gating:max="1100">
      <data-type:parameter data-type:name="FL4-A" />
    </gating:dimension>
  </gating:RectangleGate>
  
  <!-- The FL1(CD45.1)/FL4(CD45.2) gate defining recipient-derived viable leukocytes -->
  <gating:RectangleGate 
    gating:id="Recipient-derived_Viable_Leukocytes" 
    gating:parent_id="Viable_Leukocytes">
    <gating:dimension gating:max="2000">
      <data-type:parameter data-type:name="FL1-A" />
    </gating:dimension>
    <gating:dimension gating:min="520" gating:max="7800">
      <data-type:parameter data-type:name="FL4-A" />
    </gating:dimension>
  </gating:RectangleGate>
  
  <!-- The FL6(B200)/FL2(Gr1-CD11b) gate defining doner-derived B-cells -->
  <gating:RectangleGate 
    gating:id="doner-derived_B-cells"
    gating:parent_id="Donor-derived_Viable_Leukocytes">
    <gating:dimension gating:min="300">
      <data-type:parameter data-type:name="FL6-A" />
    </gating:dimension>
    <gating:dimension gating:max="1300">
      <data-type:parameter data-type:name="FL2-A" />
    </gating:dimension>
  </gating:RectangleGate>
  
  <!-- The FL6(B200)/FL3(CD4-CD8) gate defining doner-derived T-cells -->
  <gating:RectangleGate 
    gating:id="doner-derived_T-cells"
    gating:parent_id="Donor-derived_Viable_Leukocytes">
    <gating:dimension gating:max="200">
      <data-type:parameter data-type:name="FL6-A" />
    </gating:dimension>
    <gating:dimension gating:min="600">
      <data-type:parameter data-type:name="FL3-A" />
    </gating:dimension>
  </gating:RectangleGate>
  
  <!-- The FL6(B200)/FL2(Gr1-CD11b) gate defining doner-derived myeloid cells -->
  <gating:RectangleGate 
    gating:id="doner-derived_myeloid-cells"
    gating:parent_id="Donor-derived_Viable_Leukocytes">
    <gating:dimension gating:max="300">
      <data-type:parameter data-type:name="FL6-A" />
    </gating:dimension>
    <gating:dimension gating:min="1300">
      <data-type:parameter data-type:name="FL2-A" />
    </gating:dimension>
  </gating:RectangleGate>
                  
</gating:Gating-ML>

