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Export OME-NGFF metadata #107

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c7172d9
Added basic structure of NGFF metadata
XanthosXanthopoulos Feb 12, 2024
e4fa11f
Bump mypy version
XanthosXanthopoulos Feb 26, 2024
7dcdb34
Translate OME-XML pyramid metadata to NGFF Multiscale
XanthosXanthopoulos Feb 26, 2024
36a5bee
Drop mypy version to match the minimum python version requirement
XanthosXanthopoulos Feb 26, 2024
fb03f1e
Generate plate and well metadata from OME
XanthosXanthopoulos Feb 28, 2024
66bebea
Add placeholder implementation for ngff metadata
XanthosXanthopoulos Feb 29, 2024
2b4f2fa
Add handling for OME properties which are not always lists
XanthosXanthopoulos Feb 29, 2024
0d8e2bb
Add basic ngff plate metadata test
XanthosXanthopoulos Feb 29, 2024
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,6 @@ repos:
hooks:
- id: ruff
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v0.991
rev: v1.4.1
hooks:
- id: mypy
37 changes: 37 additions & 0 deletions tests/data/ome-metadata/hcs.ome.xml
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@@ -0,0 +1,37 @@
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
<Plate ID="Plate:1" Name="Control Plate" ColumnNamingConvention="letter" RowNamingConvention="number" Columns="12"
Rows="8">
<Description/>
<!-- repeat Well for # of wells in the plate that contain images -->
<Well ID="Well:1" Column="0" Row="0">
<!-- repeat WellSample for # of images taken in the well -->
<WellSample ID="WellSample:1" Index="0">
<!--
if there is an image associated with this SPW:WellSample
it is linked using an ImageRef
-->
<ImageRef ID="Image:0"/>
</WellSample>
</Well>
</Plate>
<!-- plus one more Plate for each Plate in this set -->
<!-- Screen is not required -->
<!-- The Image element follows the structure for the OME Compliant File Specification -->
<Image ID="Image:0" Name="Series 1">
<AcquisitionDate>2008-02-06T13:43:19</AcquisitionDate>
<Description>An example OME compliant file, based on Olympus.oib</Description>
<Pixels DimensionOrder="XYCZT" ID="Pixels:0" PhysicalSizeX="0.207" PhysicalSizeY="0.207" SizeC="3" SizeT="16"
SizeX="1024" SizeY="1024" SizeZ="1" TimeIncrement="120.1302" Type="uint16">
<Channel EmissionWavelength="523" ExcitationWavelength="488" ID="Channel:0:0"
IlluminationType="Epifluorescence" Name="CH1" SamplesPerPixel="1" PinholeSize="103.5"
AcquisitionMode="LaserScanningConfocalMicroscopy"/>
<Channel EmissionWavelength="578" ExcitationWavelength="561" ID="Channel:0:1"
IlluminationType="Epifluorescence" Name="CH3" SamplesPerPixel="1" PinholeSize="127.24"
AcquisitionMode="LaserScanningConfocalMicroscopy"/>
<Channel ExcitationWavelength="488" ID="Channel:0:2" IlluminationType="Transmitted" ContrastMethod="DIC"
Name="TD1" SamplesPerPixel="1" AcquisitionMode="LaserScanningConfocalMicroscopy"/>
<BinData BigEndian="false" Length="0"/>
</Pixels>
</Image>
</OME>
161 changes: 161 additions & 0 deletions tests/data/ome-metadata/one-screen-one-plate-four-wells.ome.xml
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<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
<Plate ID="Plate:1">
<Description>Plate 1 description.</Description>
<Well ID="Well:1.1.1" Column="1" Row="1">
<WellSample ID="WellSample:1.1.1.1" Index="1">
<ImageRef ID="Image:0"/>
</WellSample>
<WellSample ID="WellSample:1.1.1.2" Index="5">
<ImageRef ID="Image:1"/>
</WellSample>
<ReagentRef ID="Reagent:1"/>
</Well>
<Well ID="Well:1.2.1" Column="2" Row="1">
<WellSample ID="WellSample:1.2.1.1" Index="2">
<ImageRef ID="Image:2"/>
</WellSample>
<WellSample ID="WellSample:1.2.1.2" Index="6">
<ImageRef ID="Image:3"/>
</WellSample>
<ReagentRef ID="Reagent:1"/>
</Well>
<Well ID="Well:1.1.2" Column="1" Row="2">
<WellSample ID="WellSample:1.1.2.1" Index="3">
<ImageRef ID="Image:4"/>
</WellSample>
<WellSample ID="WellSample:1.1.2.2" Index="7">
<ImageRef ID="Image:5"/>
</WellSample>
<WellSample ID="WellSample:1.1.2.3" Index="11">
<ImageRef ID="Image:6"/>
</WellSample>
<WellSample ID="WellSample:1.1.2.4" Index="15">
<ImageRef ID="Image:7"/>
</WellSample>
<WellSample ID="WellSample:1.1.2.5" Index="19">
<ImageRef ID="Image:8"/>
</WellSample>
<ReagentRef ID="Reagent:1"/>
</Well>
<Well ID="Well:1.2.2" Column="2" Row="2">
<WellSample ID="WellSample:1.2.2.1" Index="4">
<ImageRef ID="Image:9"/>
</WellSample>
<WellSample ID="WellSample:1.2.2.2" Index="8">
<ImageRef ID="Image:10"/>
</WellSample>
<ReagentRef ID="Reagent:1"/>
</Well>
<PlateAcquisition ID="PlateAcquisition:Plate:1:ScreenAcquisition:1" StartTime="2010-02-23T12:49:30"
EndTime="2010-02-23T12:50:30">
<WellSampleRef ID="WellSample:1.1.1.1"/>
<WellSampleRef ID="WellSample:1.2.1.1"/>
<WellSampleRef ID="WellSample:1.1.2.1"/>
<WellSampleRef ID="WellSample:1.2.2.1"/>
</PlateAcquisition>
<PlateAcquisition ID="PlateAcquisition:Plate:1:ScreenAcquisition:2" StartTime="2010-02-23T12:50:30"
EndTime="2010-02-23T12:51:29">
<WellSampleRef ID="WellSample:1.1.1.2"/>
<WellSampleRef ID="WellSample:1.2.1.2"/>
<WellSampleRef ID="WellSample:1.1.2.2"/>
<WellSampleRef ID="WellSample:1.2.2.2"/>
</PlateAcquisition>
</Plate>
<Screen ID="Screen:1" ProtocolDescription="" ProtocolIdentifier="" ReagentSetDescription="" ReagentSetIdentifier=""
Name="" Type="">
<Description/>
<Reagent ID="Reagent:1" Name="" ReagentIdentifier="">
<Description/>
</Reagent>
<PlateRef ID="Plate:1"/>
</Screen>
<Image ID="Image:0" Name="6x6x1x8-swatch.tif">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:0:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:0"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:1" Name="6x6x1x8-swatch.tif-1">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:1:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:1"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:2" Name="6x6x1x8-swatch.tif-2">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:2:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:2"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:3" Name="6x6x1x8-swatch.tif-3">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:3:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:3"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:4" Name="6x6x1x8-swatch.tif-4">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:4:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:4"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:5" Name="6x6x1x8-swatch.tif-5">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:5:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:5"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:6" Name="6x6x1x8-swatch.tif-6">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:6:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:6"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:7" Name="6x6x1x8-swatch.tif-7">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:7:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:7"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:8" Name="6x6x1x8-swatch.tif-8">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:8:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:8"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:9" Name="6x6x1x8-swatch.tif-9">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:9:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:9"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
<Image ID="Image:10" Name="6x6x1x8-swatch.tif-10">
<AcquisitionDate>2010-02-23T12:51:30</AcquisitionDate>
<Pixels DimensionOrder="XYCZT" ID="Pixels:10:0" PhysicalSizeX="10000.0" PhysicalSizeY="10000.0" Type="uint8"
SizeC="1" SizeT="1" SizeX="6" SizeY="4" SizeZ="1">
<Channel Color="-2147483648" ID="Channel:10"/>
<BinData BigEndian="false" Length="32">/wCrzur//wB5oMPi/wBIbJO3AP8ePGCF</BinData>
</Pixels>
</Image>
</OME>
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