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Thread: Creating tile experiment file in OAD

  1. #1
    Junior Member
    Join Date
    Mar 2016
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    11

    Creating tile experiment file in OAD

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    Forget this post, I did a mistake with the image size. However, how can I find the z focus position of the preview image ? Also how can I set the magnification on an AxioZoom ?
    Thanks
    Philippe

    Hi,
    I trying to use OAD macro-environment to detect brain sections on slide and acquire tile regions automatically. To do that, I define a tile acquisition outlining all sections on the slide, then perform a preview image and save the stitched image. On this image I run ImageJ macro to detect slices, compute the bounding boxes for each sections and convert coordinates to stage positions (as in rare event detection macro example) and generate a tile experiment file (.czsh) . Then, I import the tile experiment file to run the acquisition. However, first the Z focus is empty using zPosition = image.Metadata.FocusPosition.split(" "); second the stage position seems not good. In the below tile exp file the tile named #section1 is calculated with the macro and the tile named TR1 is manually define. I done similar rare event detection with success using list position points. My question is the preview image have correct metadata as the "classical" image acquisition ?
    Philippe

    <?xml version="1.0" encoding="utf-8"?>
    <SampleHolder>
    <Overlap>0.1</Overlap>
    <ScanMode>Meander</ScanMode>
    <PositionedRegionsScanMode>FirstYThenX</PositionedRegionsScanMode>
    <TemplateShapesScanMode>Meander</TemplateShapesScanMode>
    <IsConstantTiles>false</IsConstantTiles>
    <TileRegionAnchorMode>Center</TileRegionAnchorMode>
    <StageReferencePoint>0,0</StageReferencePoint>
    <UseStageBacklashCorrection>true</UseStageBacklashCorrection>
    <UseFocusBacklashCorrection>true</UseFocusBacklashCorrection>
    <IsOptimizedPositionedRegionsSorting>true</IsOptimizedPositionedRegionsSorting>
    <IsOptimizedTemplateShapesSorting>true</IsOptimizedTemplateShapesSorting>
    <UseStageContinualSpeed>false</UseStageContinualSpeed>
    <StageContinualSpeed>1</StageContinualSpeed>
    <MoveToLoadPositionBetweenShapes>false</MoveToLoadPositionBetweenShapes>
    <SplitScenesInSeparateFiles>false</SplitScenesInSeparateFiles>
    <TileRegionCoveringMode>AlignedToLocalTileRegion </TileRegionCoveringMode>
    <TemplateShapesFillMode>FillGrade</TemplateShapesFillMode>
    <TemplateShapesFillGrade>0.25</TemplateShapesFillGrade>
    <TemplateShapesFillWidth>10</TemplateShapesFillWidth>
    <TemplateShapesFillHeight>10</TemplateShapesFillHeight>
    <IsOnlineStitchingEnabled>false</IsOnlineStitchingEnabled>
    <IsOnlinePyramidEnabled>true</IsOnlinePyramidEnabled>
    <GlobalInterpolationExpansionDegree>2</GlobalInterpolationExpansionDegree>
    <LocalInterpolationExpansionDegree>2</LocalInterpolationExpansionDegree>
    <IsFocusSurfaceOutlierRemovingEnabled>true</IsFocusSurfaceOutlierRemovingEnabled>
    <FocusSurfaceOutlierExpansionDegree>1</FocusSurfaceOutlierExpansionDegree>
    <FocusSurfaceOutlierThresholdSigma>2.5</FocusSurfaceOutlierThresholdSigma>
    <DelayAfterStageMove>0</DelayAfterStageMove>
    <OnlineStitchingParameter>
    <UseFocusReferenceChannel>true</UseFocusReferenceChannel>
    <ReferenceChannelId>0</ReferenceChannelId>
    </OnlineStitchingParameter>
    <AllowedScanArea IsActivated="false">
    <ContourType>Rectangle</ContourType>
    <Center>0,0</Center>
    <Size>0,0</Size>
    </AllowedScanArea>
    <TileRegions>
    <TileRegion Name="#Section1" Id="66666601126">
    <CenterPosition>85239.677,53606.76</CenterPosition>
    <ContourSize>15777.64,9996.274</ContourSize>
    <Columns>14</Columns>
    <Rows>9</Rows>
    <Z>-140000</Z>
    <TemplateShapeId></TemplateShapeId>
    <IsUsedForAcquisition>true</IsUsedForAcquisition>
    <IsProtected>false</IsProtected>
    <AreSupportPointsOutsideContourAllowed>false</AreSupportPointsOutsideContourAllowed>
    <PreferSupportPointsZ>false</PreferSupportPointsZ>
    <Contour Type="Rectangle" />
    <SupportPoints />
    </TileRegion>
    <TileRegion Name="#Section2" Id="666666119322">
    <CenterPosition>85331.515,71580.674</CenterPosition>
    <ContourSize>15333.541,10072.982</ContourSize>
    <Columns>13</Columns>
    <Rows>9</Rows>
    <Z>-140000</Z>
    <TemplateShapeId></TemplateShapeId>
    <IsUsedForAcquisition>true</IsUsedForAcquisition>
    <IsProtected>false</IsProtected>
    <AreSupportPointsOutsideContourAllowed>false</AreSupportPointsOutsideContourAllowed>
    <PreferSupportPointsZ>false</PreferSupportPointsZ>
    <Contour Type="Rectangle" />
    <SupportPoints />
    </TileRegion>
    <TileRegion Name="#Section3" Id="666666219023">
    <CenterPosition>90877.702,71590.767</CenterPosition>
    <ContourSize>15951.242,10145.652</ContourSize>
    <Columns>14</Columns>
    <Rows>9</Rows>
    <Z>-140000</Z>
    <TemplateShapeId></TemplateShapeId>
    <IsUsedForAcquisition>true</IsUsedForAcquisition>
    <IsProtected>false</IsProtected>
    <AreSupportPointsOutsideContourAllowed>false</AreSupportPointsOutsideContourAllowed>
    <PreferSupportPointsZ>false</PreferSupportPointsZ>
    <Contour Type="Rectangle" />
    <SupportPoints />
    </TileRegion>
    <TileRegion Name="#Section4" Id="66666631376">
    <CenterPosition>90884.757,54020.58</CenterPosition>
    <ContourSize>16104.659,9875.155</ContourSize>
    <Columns>14</Columns>
    <Rows>9</Rows>
    <Z>-140000</Z>
    <TemplateShapeId></TemplateShapeId>
    <IsUsedForAcquisition>true</IsUsedForAcquisition>
    <IsProtected>false</IsProtected>
    <AreSupportPointsOutsideContourAllowed>false</AreSupportPointsOutsideContourAllowed>
    <PreferSupportPointsZ>false</PreferSupportPointsZ>
    <Contour Type="Rectangle" />
    <SupportPoints />
    </TileRegion>
    <TileRegion Name="TR1" Id="636548953094173634">
    <CenterPosition>76952.198,43067.118</CenterPosition>
    <ContourSize>16527.196,11795.412</ContourSize>
    <Columns>14</Columns>
    <Rows>10</Rows>
    <Z>-147275</Z>
    <TemplateShapeId></TemplateShapeId>
    <IsUsedForAcquisition>true</IsUsedForAcquisition>
    <IsProtected>false</IsProtected>
    <AreSupportPointsOutsideContourAllowed>false</AreSupportPointsOutsideContourAllowed>
    <PreferSupportPointsZ>false</PreferSupportPointsZ>
    <Contour Type="Rectangle" />
    <SupportPoints />
    </TileRegion>
    </TileRegions>
    <SingleTileRegions />
    <SingleTileRegionArrays />
    </SampleHolder>
    Last edited by phm; 02-23-2018 at 03:56 PM.

  2. #2
    CZ Administrators Carl Zeiss Microscopy 3's Avatar
    Join Date
    Jan 2013
    Posts
    388
    how can I find the z focus position of the preview image ? Also how can I set the magnification on an AxioZoom ?
    The z-focus position can be found in the metadata of the image.
    An alternative might be to have a look at Zen.Devices.Focus etc.

    The magnification is in the experiment setting, which is an XML.
    To change the magnification you have to modify the XML file and load the experiment again.

    I hope this helps ...

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