Extractin Channels from czi image sets

dhavas

Hi,

I have the problem that I want to extract a channel from CZI images to run automated analyses.

First steps are simple and should include:

Extraction of one channel, making an 8bit grey scale of if and work on it.

It opens in color composite view. If I subsample it is dependent on the view. When I record macro, I always get the error that methods are not found, thus I can't automate:

In this case: Active RegionInUse not found:

With New MediaCy.Viewers.Set.ImageSetViewOptionsCommand(grrrr)
            .ActiveRegionInUse = MediaCy.IQL.Sets.mcImageSetActivePortionTypes.mcisaptActiveDisplayRegion
            .Run(window1)
        End With

or other method (changing view, directly switch channel and extract grey scale)

Public Function Grr2() As SimpleScript
        Grr2 = New SimpleScript
        Dim var1 = "6_15_L17_2", doc1, window1, image1, doc2

        With Application.DocumentCommands.Activate(Grr2)
            .Run(var1, doc1)
        End With

        With Application.WindowCommands.Define(Grr2)
            .Run(doc1, window1)
        End With

        With New MediaCy.Viewers.Set.ImageSetViewOptionsCommand(Grr2)
            .ColorCompositeView = False
            .Run(window1)
        End With

        With Application.DocumentCommands.Activate(Grr2)
            .Run(doc1, doc1)
        End With

        With New MediaCy.Viewers.Set.ImageSetViewOptionsCommand(Grr2)
            .ViewLocation = New McImageSetLocations
            .ViewLocation.Add(mcImageSetDimensions.mcisdChannel, 1)
            .Run(window1)
        End With

        With Application.RibbonCommands.SelectRibbonTab(Grr2)
            .TabName = "Adjust"
            .Run()
        End With

        With Adjust.ImageCommands.Convert(Grr2)
            .Destination = Image.ConvertTypes.Mono8
            .ConvertOption = Image.ConvertOptions.Custom
            .SourceRange = New RangeD(0R, 4096R)
            .DestinationRange = New RangeD(0R, 255R)
            .Visible = True
            .Run(doc1, image1)
        End With

        With Application.DocumentCommands.Activate(Grr2)
            .Run(image1, doc2)
        End With

    End Function

In this case the method .colorCompositeView is not found if repeating the script. 

In detail: MediaCy.IQL.Application.McCommandExtended.ColorCompositeView not found...

Is there some lib to integrate that those commands work?

Many thx

Daniel

YuriG

Hi Dan,

It looks like there is a problem with that command in 9.1.4. We are going to release a new Premier version pretty soon, but right now you can use the attached project, which shows how to extract all Z-stacks from image set without using that command:

    Public Sub ExtractZStacksFromActiveImage
        Dim imset As MediaCy.IQL.Sets.McImageSet=ThisApplication.ActiveDocument.Data
        If imset Is Nothing Then Exit Sub'this is not image set
        'get number of channels in stack
        Dim nChannels As Long=imset.GetDimensionLength(mcImageSetDimensions.mcisdChannel,imset.GetCurrentLocation)
        For chInd As Integer=0 To nChannels-1
            ExtractZStackFromChannel(imset,chInd)
        Next
    End Sub


    Public Sub ExtractZStackFromChannel(imset As MediaCy.IQL.Sets.McImageSet,chInd As Long)
        Dim setLoc As New MediaCy.IQL.Sets.McImageSetLocations
        'select channel to location
        setLoc.Add(mcImageSetDimensions.mcisdChannel, chInd)
        'get number of frames in Z dimension
        Dim nZframes As Long=imset.GetDimensionLength(mcImageSetDimensions.mcisdZ,setLoc)

        'create region to extract
        Dim theRegion As MediaCy.IQL.Sets.McImageSetRegion=ThisApplication.CreateOperator("McImageSetLib.McImageSetRegion")
        Dim theSections As MediaCy.IQL.Sets.McImageSetSections = theRegion.Sections
        theSections.Add(mcImageSetDimensions.mcisdChannel,chInd,1)
        theSections.Add(mcImageSetDimensions.mcisdZ,0,nZframes)
        'create image of Z frames (invisible)
        Dim outIm As McImage=imset.ExtractImage(theRegion, mcImageCreateFlags.mcicfNotVisible Or mcImageCreateFlags.mcicfNoAddToCollection)
        'show image
        outIm.Visible=True
    End Sub

Let me know if it will work for you,

Regards,

Yuri

YuriG

Hi Daniel,

What version of Premier do you have? The current version is 9.1.4, it can be updated automatically at startup.

Please try the macro below, that works in 9.1.4:

    Public Function ExtractActiveChannel() As SimpleScript
        ExtractActiveChannel = New SimpleScript
        Dim doc1, spcal1, window1, image1, doc2, image2, doc3

        With Application.DocumentCommands.Active(AutoThreshold)
            .Run(doc1)
        End With


        With Application.WindowCommands.Define(ExtractActiveChannel)
            .Run(doc1, window1)
        End With

        With New MediaCy.Viewers.Set.ImageSetViewOptionsCommand(ExtractActiveChannel)
            .ColorCompositeView = False
            .Run(window1)
        End With

        With Adjust.ImageSetCommands.ExtractDimension(ExtractActiveChannel)
            .Dimension = MediaCy.IQL.Sets.mcImageSetDimensions.mcisdDefault
            .Run(doc1, image1)
        End With

        With Application.DocumentCommands.Activate(ExtractActiveChannel)
            .Run(image1, doc2)
        End With

        With Adjust.ImageCommands.Convert(ExtractActiveChannel)
            .Destination = Image.ConvertTypes.Mono8
            .ConvertOption = Image.ConvertOptions.Scale
            .Visible = True
            .Run(doc2, image2)
        End With

        With Application.DocumentCommands.Activate(ExtractActiveChannel)
            .Run(image2, doc3)
        End With

    End Function

Regards,

Yuri

dhavas

Thanks Yuri,

According to SW it's version 9.1.5638.4....Premier 3D version.

Now type identifier invalid in line

With New MediaCy.Viewers.Set.ImageSetViewOptionsCommand(ExtractActiveChannel)

Those are imported - something missing?

Imports MediaCy.Addins.SCalibration.Commands
Imports MediaCy.Addins.Scripting
Imports MediaCy.Addins.SCalibration
Imports MediaCy.Addins.Scripting.Workflow
Imports MediaCy.Viewers.Image
Imports MediaCy.Viewers.Set
Imports MediaCy.IQL.Sets

YuriG

Hi Daniel,

It could be that the version you have doesn't have definition for ImageSetViewOptionsCommand (there was a bug about it).
To verify that please try to disable this command (comment it out):

       With New MediaCy.Viewers.Set.ImageSetViewOptionsCommand(ExtractActiveChannel)
            .ColorCompositeView = False
            .Run(window1)
        End With

Let me know if that's fixed the error.

Regards,

Yuri 

dhavas

Hi Yuri,

did not fix it. now

.Dimension = MediaCy.IQL.Sets.mcImageSetDimensions.mcisdDefault

in the next with block returns that a valid data type is expected.

Thus the MediaCy.IQL.Sets.mcImageSetDimensions.mcisdDefault object is not found.

If I replace with integer 0 then it extracts a set with both channels, 1 to 4 different dimensions of channel 1. 5 upwards always channel 1 (gave up at six)

However, at least with 0 I can work if I can switch in the set.

Best

Dan