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imagejanimagejan
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Merge pull request #190 from fmi-faim/migrate-eicm
Migrate https://github.com/fmi-faim/eicm to faim-ipa.
2 parents 5f2ddbf + 066fd46 commit 74226f4

16 files changed

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‎resources/eicm/MeasurementDetail.mrf

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<?xml version="1.0" encoding="utf-8"?>
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<bts:MeasurementDetail bts:Version="1.0" bts:OperatorName="reitsabi" bts:Title="20221221-Field-illumination-QC" bts:Application="" bts:BeginTime="2022-12-21T14:39:35.8551584+01:00" bts:EndTime="2022-12-21T14:55:54.7397183+01:00" bts:MeasurementSettingFileName="QC_dyes_60x__Cellvis_glass.mes" bts:ColumnCount="12" bts:RowCount="8" bts:TimePointCount="4" bts:FieldCount="16" bts:ZCount="36" bts:TargetSystem="CV7000 FM03" bts:ReleaseNumber="R2.02.07" bts:Status="0" xmlns:bts="http://www.yokogawa.co.jp/BTS/BTSSchema/1.0">
3+
<bts:MeasurementSamplePlate bts:Name="Dyes_60xW_Cellvis" bts:WellPlateFileName="Dyes_60xW_Cellvis.wpi" bts:WellPlateProductFileName="1009680002_Cellvis_#P96-1.5H-N.wpp" />
4+
<bts:MeasurementChannel bts:Ch="1" bts:HorizontalPixelDimension="0.10833333333333334" bts:VerticalPixelDimension="0.10833333333333334" bts:CameraNumber="2" bts:InputBitDepth="16" bts:InputLevel="5000" bts:HorizontalPixels="2560" bts:VerticalPixels="2160" bts:FilterWheelPosition="5" bts:FilterPosition="1" bts:ShadingCorrectionSource="SC_BP445-45_60xW_M01_CH01.tif" bts:ObjectiveMagnificationRatio="1" bts:OriginalHorizontalPixels="2560" bts:OriginalVerticalPixels="2160" />
5+
<bts:MeasurementChannel bts:Ch="2" bts:HorizontalPixelDimension="0.10833333333333334" bts:VerticalPixelDimension="0.10833333333333334" bts:CameraNumber="2" bts:InputBitDepth="16" bts:InputLevel="10000" bts:HorizontalPixels="2560" bts:VerticalPixels="2160" bts:FilterWheelPosition="5" bts:FilterPosition="2" bts:ShadingCorrectionSource="SC_BP525-50_60xW_M01_CH02.tif" bts:ObjectiveMagnificationRatio="1" bts:OriginalHorizontalPixels="2560" bts:OriginalVerticalPixels="2160" />
6+
<bts:MeasurementChannel bts:Ch="3" bts:HorizontalPixelDimension="0.10833333333333334" bts:VerticalPixelDimension="0.10833333333333334" bts:CameraNumber="1" bts:InputBitDepth="16" bts:InputLevel="10000" bts:HorizontalPixels="2560" bts:VerticalPixels="2160" bts:FilterWheelPosition="4" bts:FilterPosition="1" bts:ShadingCorrectionSource="SC_BP600-37_60xW_M01_CH03.tif" bts:ObjectiveMagnificationRatio="1" bts:OriginalHorizontalPixels="2560" bts:OriginalVerticalPixels="2160" />
7+
<bts:MeasurementChannel bts:Ch="4" bts:HorizontalPixelDimension="0.10833333333333334" bts:VerticalPixelDimension="0.10833333333333334" bts:CameraNumber="1" bts:InputBitDepth="16" bts:InputLevel="10000" bts:HorizontalPixels="2560" bts:VerticalPixels="2160" bts:FilterWheelPosition="4" bts:FilterPosition="2" bts:ShadingCorrectionSource="SC_BP676-29_60xW_M01_CH04.tif" bts:ObjectiveMagnificationRatio="1" bts:OriginalHorizontalPixels="2560" bts:OriginalVerticalPixels="2160" />
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<bts:MeasurementChannel bts:Ch="5" bts:HorizontalPixelDimension="0.10833333333333334" bts:VerticalPixelDimension="0.10833333333333334" bts:CameraNumber="2" bts:InputBitDepth="16" bts:InputLevel="10000" bts:HorizontalPixels="2560" bts:VerticalPixels="2160" bts:FilterWheelPosition="5" bts:FilterPosition="2" bts:ShadingCorrectionSource="" bts:ObjectiveMagnificationRatio="1" bts:OriginalHorizontalPixels="2560" bts:OriginalVerticalPixels="2160" />
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<bts:MeasurementChannel bts:Ch="6" bts:HorizontalPixelDimension="0.10833333333333334" bts:VerticalPixelDimension="0.10833333333333334" bts:CameraNumber="2" bts:InputBitDepth="16" bts:InputLevel="65535" bts:HorizontalPixels="2560" bts:VerticalPixels="2160" bts:FilterWheelPosition="5" bts:FilterPosition="2" bts:ShadingCorrectionSource="SC_BP525-50_60xW_M01_CH06.tif" bts:ObjectiveMagnificationRatio="1" bts:OriginalHorizontalPixels="2560" bts:OriginalVerticalPixels="2160" />
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</bts:MeasurementDetail>

‎resources/eicm/QC_dyes_60x__Cellvis_glass.mes

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<?xml version="1.0" encoding="utf-8"?>
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<bts:MeasurementSetting bts:Version="1.0" bts:ProductID="1009680002" bts:Application="" bts:Columns="12" bts:Rows="8" xmlns:bts="http://www.yokogawa.co.jp/BTS/BTSSchema/1.0">
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<bts:Timelapse>
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<bts:Timeline bts:Name="Time Line 1" bts:InitialTime="0" bts:Period="496" bts:Interval="496" bts:ExpectedTime="496" bts:Color="#ff44ee66" bts:OverrideExpectedTime="false">
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<bts:WellSequence bts:IsSelected="true">
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<bts:TargetWell bts:Column="10" bts:Row="6">true</bts:TargetWell>
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</bts:WellSequence>
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<bts:PointSequence bts:Method="FixedPosition">
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<bts:FixedPosition bts:IsProportional="false">
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<bts:Point bts:X="-1350" bts:Y="-1350" />
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</bts:FixedPosition>
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</bts:PointSequence>
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<bts:ActionList bts:RunMode="sequential" bts:AFSearch="bottom">
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<bts:ActionAcquire3D bts:XOffset="0" bts:YOffset="0" bts:AFShiftBase="-2" bts:TopDistance="20" bts:BottomDistance="-15" bts:SliceLength="1" bts:UseSoftFocus="false">
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<bts:Ch>1</bts:Ch>
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</bts:ActionAcquire3D>
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</bts:ActionList>
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</bts:Timeline>
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<bts:Timeline bts:Name="Time Line 2" bts:InitialTime="865" bts:Period="290" bts:Interval="0" bts:ExpectedTime="190" bts:Color="#ff44ee66" bts:OverrideExpectedTime="false">
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<bts:WellSequence bts:IsSelected="true">
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<bts:TargetWell bts:Column="10" bts:Row="3">true</bts:TargetWell>
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</bts:WellSequence>
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<bts:PointSequence bts:Method="FixedPosition">
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<bts:FixedPosition bts:IsProportional="false">
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<bts:Point bts:X="-1350" bts:Y="1350" />
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<bts:Point bts:X="-450" bts:Y="1350" />
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<bts:Point bts:X="1350" bts:Y="450" />
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<bts:Point bts:X="-1350" bts:Y="-450" />
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<bts:Point bts:X="-450" bts:Y="-450" />
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<bts:Point bts:X="450" bts:Y="-450" />
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<bts:Point bts:X="1350" bts:Y="-450" />
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<bts:Point bts:X="1350" bts:Y="-1350" />
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<bts:Point bts:X="450" bts:Y="-1350" />
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<bts:Point bts:X="-450" bts:Y="-1350" />
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<bts:Point bts:X="-1350" bts:Y="-1350" />
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</bts:FixedPosition>
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</bts:PointSequence>
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<bts:ActionList bts:RunMode="sequential" bts:AFSearch="bottom">
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<bts:ActionAcquire3D bts:XOffset="0" bts:YOffset="0" bts:AFShiftBase="-2" bts:TopDistance="20" bts:BottomDistance="-15" bts:SliceLength="1" bts:UseSoftFocus="false">
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<bts:Ch>2</bts:Ch>
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</bts:ActionAcquire3D>
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</bts:ActionList>
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</bts:Timeline>
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<bts:Timeline bts:Name="Time Line 3" bts:InitialTime="496" bts:Period="329" bts:Interval="0" bts:ExpectedTime="179" bts:Color="#ff44ee66" bts:OverrideExpectedTime="false">
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<bts:WellSequence bts:IsSelected="true">
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<bts:TargetWell bts:Column="10" bts:Row="4">true</bts:TargetWell>
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</bts:WellSequence>
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<bts:PointSequence bts:Method="FixedPosition">
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<bts:FixedPosition bts:IsProportional="false">
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<bts:Point bts:X="-1350" bts:Y="1350" />
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<bts:Point bts:X="-450" bts:Y="1350" />
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<bts:Point bts:X="1350" bts:Y="450" />
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<bts:Point bts:X="-450" bts:Y="450" />
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<bts:Point bts:X="-1350" bts:Y="450" />
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<bts:Point bts:X="-1350" bts:Y="-450" />
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<bts:Point bts:X="-450" bts:Y="-450" />
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<bts:Point bts:X="450" bts:Y="-450" />
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<bts:Point bts:X="1350" bts:Y="-450" />
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<bts:Point bts:X="1350" bts:Y="-1350" />
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<bts:Point bts:X="450" bts:Y="-1350" />
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<bts:Point bts:X="-450" bts:Y="-1350" />
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<bts:Point bts:X="-1350" bts:Y="-1350" />
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</bts:FixedPosition>
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</bts:PointSequence>
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<bts:ActionList bts:RunMode="sequential" bts:AFSearch="bottom">
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<bts:ActionAcquire3D bts:XOffset="0" bts:YOffset="0" bts:AFShiftBase="-2" bts:TopDistance="20" bts:BottomDistance="-15" bts:SliceLength="1" bts:UseSoftFocus="false">
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<bts:Ch>3</bts:Ch>
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</bts:ActionAcquire3D>
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</bts:ActionList>
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</bts:Timeline>
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<bts:Timeline bts:Name="Time Line 4" bts:InitialTime="675" bts:Period="329" bts:Interval="0" bts:ExpectedTime="190" bts:Color="#ff44ee66" bts:OverrideExpectedTime="false">
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<bts:WellSequence bts:IsSelected="true">
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<bts:TargetWell bts:Column="10" bts:Row="5">true</bts:TargetWell>
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</bts:WellSequence>
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<bts:PointSequence bts:Method="FixedPosition">
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<bts:FixedPosition bts:IsProportional="false">
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<bts:Point bts:X="-1350" bts:Y="1350" />
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<bts:Point bts:X="-450" bts:Y="1350" />
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<bts:Point bts:X="450" bts:Y="1350" />
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<bts:Point bts:X="1350" bts:Y="1350" />
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<bts:Point bts:X="1350" bts:Y="450" />
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<bts:Point bts:X="450" bts:Y="450" />
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<bts:Point bts:X="-450" bts:Y="450" />
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<bts:Point bts:X="-1350" bts:Y="450" />
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<bts:Point bts:X="-1350" bts:Y="-450" />
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<bts:Point bts:X="-450" bts:Y="-450" />
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<bts:Point bts:X="450" bts:Y="-450" />
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<bts:Point bts:X="1350" bts:Y="-450" />
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<bts:Point bts:X="1350" bts:Y="-1350" />
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<bts:Point bts:X="450" bts:Y="-1350" />
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<bts:Point bts:X="-450" bts:Y="-1350" />
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<bts:Point bts:X="-1350" bts:Y="-1350" />
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</bts:FixedPosition>
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</bts:PointSequence>
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<bts:ActionList bts:RunMode="sequential" bts:AFSearch="bottom">
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<bts:ActionAcquire3D bts:XOffset="0" bts:YOffset="0" bts:AFShiftBase="-2" bts:TopDistance="20" bts:BottomDistance="-15" bts:SliceLength="1" bts:UseSoftFocus="false">
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<bts:Ch>4</bts:Ch>
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</bts:ActionAcquire3D>
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</bts:ActionList>
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</bts:Timeline>
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</bts:Timelapse>
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<bts:LightSourceList>
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<bts:LightSource bts:Name="405nm" bts:Type="Laser" bts:WaveLength="405" bts:Power="100" />
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<bts:LightSource bts:Name="488nm" bts:Type="Laser" bts:WaveLength="488" bts:Power="100" />
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<bts:LightSource bts:Name="561nm" bts:Type="Laser" bts:WaveLength="561" bts:Power="100" />
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<bts:LightSource bts:Name="640nm" bts:Type="Laser" bts:WaveLength="640" bts:Power="100" />
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<bts:LightSource bts:Name="Lamp" bts:Type="Lamp" bts:WaveLength="0" bts:Power="30" />
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</bts:LightSourceList>
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<bts:ChannelList>
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<bts:Channel bts:Ch="1" bts:Target="405" bts:ObjectiveID="60004" bts:Objective="60x W" bts:Magnification="60" bts:MethodID="1" bts:Method="Confocal Fluorescence 405/488/561/640 nm" bts:FilterID="1" bts:Acquisition="BP445/45" bts:ExposureTime="600" bts:Binning="1" bts:Color="#FF1B54FF" bts:MinLevel="0" bts:MaxLevel="0.16008524507960367" bts:Kind="ConfocalFluorescence" bts:AndorParameterID="32" bts:AndorParameter="Gain 1,4" bts:CameraType="Andor" bts:InputLevel="5000" bts:Fluorophore="">
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<bts:LightSourceName>405nm</bts:LightSourceName>
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</bts:Channel>
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<bts:Channel bts:Ch="2" bts:Target="488" bts:ObjectiveID="60004" bts:Objective="60x W" bts:Magnification="60" bts:MethodID="1" bts:Method="Confocal Fluorescence 405/488/561/640 nm" bts:FilterID="2" bts:Acquisition="BP525/50" bts:ExposureTime="70" bts:Binning="1" bts:Color="#FF00FFA1" bts:MinLevel="0" bts:MaxLevel="0.79942334210856225" bts:Kind="ConfocalFluorescence" bts:AndorParameterID="32" bts:AndorParameter="Gain 1,4" bts:CameraType="Andor" bts:InputLevel="10000" bts:Fluorophore="">
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<bts:LightSourceName>488nm</bts:LightSourceName>
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</bts:Channel>
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<bts:Channel bts:Ch="3" bts:Target="561" bts:ObjectiveID="60004" bts:Objective="60x W" bts:Magnification="60" bts:MethodID="1" bts:Method="Confocal Fluorescence 405/488/561/640 nm" bts:FilterID="5" bts:Acquisition="BP600/37" bts:ExposureTime="50" bts:Binning="1" bts:Color="#FFFF8200" bts:MinLevel="0" bts:MaxLevel="0.29171367682085975" bts:Kind="ConfocalFluorescence" bts:AndorParameterID="32" bts:AndorParameter="Gain 1,4" bts:CameraType="Andor" bts:InputLevel="10000" bts:Fluorophore="">
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<bts:LightSourceName>561nm</bts:LightSourceName>
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</bts:Channel>
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<bts:Channel bts:Ch="4" bts:Target="640" bts:ObjectiveID="60004" bts:Objective="60x W" bts:Magnification="60" bts:MethodID="1" bts:Method="Confocal Fluorescence 405/488/561/640 nm" bts:FilterID="6" bts:Acquisition="BP676/29" bts:ExposureTime="70" bts:Binning="1" bts:Color="#FFFF1B00" bts:MinLevel="0" bts:MaxLevel="0.17888930675692605" bts:Kind="ConfocalFluorescence" bts:AndorParameterID="32" bts:AndorParameter="Gain 1,4" bts:CameraType="Andor" bts:InputLevel="10000" bts:Fluorophore="">
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<bts:LightSourceName>640nm</bts:LightSourceName>
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</bts:Channel>
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<bts:Channel bts:Ch="5" bts:Target="Brightfield" bts:ObjectiveID="60004" bts:Objective="60x W" bts:Magnification="60" bts:MethodID="4" bts:Method="Brightfield(confocal path)" bts:FilterID="2" bts:Acquisition="BP525/50" bts:ExposureTime="100" bts:Binning="1" bts:Color="#FFFFFFFF" bts:MinLevel="0" bts:MaxLevel="0.09862142099681849" bts:Kind="Brightfield" bts:AndorParameterID="32" bts:AndorParameter="Gain 1,4" bts:CameraType="Andor" bts:InputLevel="10000" bts:Fluorophore="">
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<bts:LightSourceName>Lamp</bts:LightSourceName>
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</bts:Channel>
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<bts:Channel bts:Ch="6" bts:Target="FITC" bts:ObjectiveID="60004" bts:Objective="60x W" bts:Magnification="60" bts:MethodID="1" bts:Method="Confocal Fluorescence 405/488/561/640 nm" bts:FilterID="2" bts:Acquisition="BP525/50" bts:ExposureTime="15" bts:Binning="1" bts:Color="#FF00FFA1" bts:MinLevel="0" bts:MaxLevel="0.79942334210856225" bts:Kind="ConfocalFluorescence" bts:AndorParameterID="32" bts:AndorParameter="Gain 1,4" bts:CameraType="Andor" bts:InputLevel="65535" bts:Fluorophore="">
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<bts:LightSourceName>488nm</bts:LightSourceName>
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</bts:Channel>
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</bts:ChannelList>
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</bts:MeasurementSetting>

‎resources/eicm/gradient-left-right.tif

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‎resources/eicm/gradient-top-bottom.tif

1.59 KB
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‎src/faim_ipa/eicm/__init__.py

Whitespace-only changes.

‎src/faim_ipa/eicm/estimator/__init__.py

Whitespace-only changes.

‎src/faim_ipa/eicm/estimator/gaussian2D_fit.py

+119
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import numpy as np
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from scipy.optimize import curve_fit
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from skimage.measure import centroid
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def ellipsoid_2D(coords, A, B, mu_x, mu_y, cxx, cxy, cyy):
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"""
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Evaluates the given ellipsoid parameters at the provided coordinates.
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:param coords: at which the evaluation takes place
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:param A: amplitude
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:param B: offset
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:param mu_x: x location of the centroid
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:param mu_y: y location of the centroid
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:param cxx: covariance matrix term at 00
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:param cxy: covariance matrix term at 01
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:param cyy: covariance matrix term at 11
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:return:
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"""
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inv = np.linalg.inv(np.array([[cxx, cxy], [cxy, cyy]]) + np.identity(2) * 1e-8)
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return (
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A
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* np.exp(
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-0.5
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* (
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inv[0, 0] * (coords[:, 1] - mu_x) ** 2
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+ 2 * inv[0, 1] * (coords[:, 1] - mu_x) * (coords[:, 0] - mu_y)
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+ inv[1, 1] * (coords[:, 0] - mu_y) ** 2
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)
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)
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+ B
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)
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def get_cov_matrix(img):
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"""
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Compute covariance matrix of the provided image.
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:param img:
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:return: covariance matrix
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"""
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def cov(x, y, i):
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return np.sum(x * y * i) / np.sum(i)
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y, x = np.meshgrid(
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np.arange(img.shape[0]),
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np.arange(img.shape[1]),
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indexing="ij",
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)
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cen = centroid(img)
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y = y.ravel() - cen[0]
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x = x.ravel() - cen[1]
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cxx = cov(x, x, img.ravel())
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cyy = cov(y, y, img.ravel())
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cxy = cov(x, y, img.ravel())
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return np.array([[cxx, cxy], [cxy, cyy]])
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def get_estimates(data):
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"""
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Estimate parameters of 2D Gaussian fit to the data.
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:param data:
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:return: (amplitude, offset, centroid-x, centroid-y, cxx, cxy, cyy)
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"""
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max_ = data.max()
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mean_ = data.mean()
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cy, cx = centroid(data)
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cov = get_cov_matrix(data)
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return [
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max_ - mean_,
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mean_,
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cx,
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cy,
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cov[0, 0],
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cov[0, 1],
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cov[1, 1],
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]
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def get_coords(data):
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"""
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Compute coordinate grid of provided 2D data.
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:param data:
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:return: coordinates
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"""
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yy = np.arange(data.shape[0])
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xx = np.arange(data.shape[1])
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y, x = np.meshgrid(yy, xx, indexing="ij")
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return np.stack([y.ravel(), x.ravel()], -1)
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def fit_gaussian_2d(data, coords):
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"""
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Fit 2D ellipsoid to data.
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:param data: intensities
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:param coords: pixel coordinates
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:return: popt, pcov (see scipy.optimize.curve_fit)
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"""
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return curve_fit(
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ellipsoid_2D,
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coords,
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data.ravel(),
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p0=get_estimates(data),
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)
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def compute_fitted_matrix(coords, ellipsoid_parameters, shape):
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"""
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Compute 2D ellipsoid for provided set of parameters
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:param coords: pixel coordinates
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:param ellipsoid_parameters:
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:param shape: of the final output
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:return: matrix
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"""
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return ellipsoid_2D(coords, *ellipsoid_parameters).reshape(shape)

‎src/faim_ipa/eicm/estimator/gaussian_blur.py

+14
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,14 @@
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import numpy as np
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from scipy.ndimage import gaussian_filter
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def create_blurred_illumination_matrix(img, sigma: float = 20):
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"""
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Takes an image and blurs it with a Gaussian.
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:param img: The acquired illumination field.
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:param sigma: Gaussian sigma.
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:return: illumination matrix
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"""
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matrix = gaussian_filter(input=img.astype(np.float32), sigma=sigma, mode="nearest")
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return matrix

‎src/faim_ipa/eicm/estimator/polynomial_fit.py

+44
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,44 @@
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import numpy as np
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3+
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def polynomial_fit(mip, polynomial_degree=3, order=None):
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"""
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Fits a polynomial f(x, y) to the provided mip.
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:param mip: to fit
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:param polynomial_degree: highest degree of individual coefficients
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:param order: polynomial order
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:return: fitted matrix, string describing the polynomial
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"""
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Y, X = np.meshgrid(
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np.linspace(0, 1, mip.shape[0]), np.linspace(0, 1, mip.shape[1]), indexing="ij"
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)
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coeffs = np.ones((polynomial_degree + 1, polynomial_degree + 1))
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A = np.zeros((coeffs.size, X.size))
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poly_str = ["1"]
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for row_idx, (i, j) in enumerate(np.ndindex(coeffs.shape)):
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if order is not None and i + j > order:
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tmp = np.zeros_like(X)
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else:
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tmp = coeffs[i, j] * X**j * Y**i
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substr = []
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if j > 0:
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substr.append(f"X^{j}")
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if i > 0:
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substr.append(f"Y^{i}")
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if len(substr) > 0:
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poly_str.append(" * ".join(substr))
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A[row_idx] = tmp.ravel()
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poly_str = " + ".join(poly_str)
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x, residuals, rank, s = np.linalg.lstsq(A.T, np.ravel(mip), rcond=None)
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x = x.reshape((polynomial_degree + 1, polynomial_degree + 1))
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fit = np.polynomial.polynomial.polyval2d(Y, X, x).reshape(mip.shape)
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return fit, poly_str

‎src/faim_ipa/eicm/estimator/utils.py

+11
Original file line numberDiff line numberDiff line change
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import numpy as np
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def normalize_matrix(matrix):
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"""
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Normalize matrix to [0, 1] by dividing it by its maximum value.
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:param matrix:
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:return: normalized matrix
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"""
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return np.clip(matrix / matrix.max(), 0.0, 1.0)

‎src/faim_ipa/eicm/preprocessing/__init__.py

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