measurement in an ROI

PaulSheppard

I want to count thresholded cells inside a free drawn ROI and get 'count per unit area.' I can threshold the cells and draw the ROI but I don't know which measurement parameters to use - I can't find the ROI area.

YuriG

Hi Paul,

The ROI Area is not reported directly. If you use a macro you can get ROI area using the following line:

  Public Sub PrintROIArea
    Debug.Print ThisApplication.ActiveImage.Aoi.mRgnArea.Sum
  End Sub

There is also a way getting this area from Percent Area measurement. 

Regards,

Yuri

mbatchelor

Paul --

I took a bit of time this (FRI) AM and created a PREMIER PROJECT that performs the TASK that you described in your question.

I have packaged this into an IPX FILE and attached that file as

    Demo-2016-11-04-094836.ipx

The PROJECT consists of two files:

    Demo-2016-11-04-094836.ipp
    Module1.vb

The CODE for MODULE1 is shown below with the DEPENDENCIES that are needed.

The DEMOMACRO FUNCTION within MODULE1 contains code to:

        'Declare LOCAL VARIABLES
        'Set up ERROR HANDLING
        'Connect with IMAGE
        'Clear MEASUREMENT LIST
        'Activate AREA MEASUREMENT
        'Set APPLY FILTERS to OFF
        'Learn OBJECT COUNT
        'Learn CALIBRATION INFORMATION
        'Learn AOI AREA (using Yuri's example + a mechanism for NO ROI)
        'Calculate OBJECT DENSITY
        'Create RESULTS STRING
        'Display RESULTS STRING in OUTPUT WINDOW
        'Send RESULTS STRING to CLIPBOARD

This FUNCTION will handle the ERROR CONDITIONS (No Objects, No ROIs, No Calibrations) that seemed to be appropriate.

This FUNCTION will also put the RESULTS STRING in the PREMIER OUTPUT WINDOW and on the WINDOWS CLIPBOARD (so they can be pasted into WORD, EXCEL, etc.).

I have also attached a SCREEN CAPTURE as

    2016-11-04-113147.jpg

That shows the general configuration and operation of this PROJECT and the appearance of the RESULTS STRING when PASTED into EXCEL.

*-*-*-*-*-

!!! PLEASE NOTE !!!

I have just realized that I goofed on the UNITS for DENSITY!

I did not include the "^2" to make the DISTANCE UNITS into AREA UNITS. 

I'm sure you can resolve this if you use this CODE.

*-*-*-*-*-

I hope this information is helpful.

-- Matt

*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

Imports MediaCy.Addins.Measurements
Imports MediaCy.Addins.Measurements.Gadgets
Imports MediaCy.Addins.Measurements.McMMData

Public Module DemoModule

    Public Function DemoMacro()

        'Declare LOCAL VARIABLES

        Dim doc1
        Dim MyData As McMMData
        Dim MyObjectCount As Double
        Dim MyCalibrationUnits As String
        Dim MyPixelSizeX As Double
        Dim MyPixelSizeY As Double
        Dim MyRoiArea As Double
        Dim MyObjectDensity As Double
        Dim MyResults As String

        'Set up error handling

        On Error Resume Next

        'Connect with IMAGE
        With Application.DocumentCommands.Active(Nothing)
            .Run(doc1)
        End With

        'Clear MEASUREMENT LIST

        With Measure.MeasurementsCommands.Options(Nothing)
            .SelMeasurements = New MeasCollection()
            .Segmentation.FilterRanges = New System.Collections.Generic.List(Of MeasFilterEntry)
            .Run(doc1)
        End With

        'Activate AREA MEASUREMENT

        With Measure.MeasurementsCommands.Options(Nothing)
            .SelMeasurements = New MeasCollection()
                .SelMeasurements.Add( New MeasEntry(eMeasures.RgnArea))
            .Segmentation.FilterRanges = New System.Collections.Generic.List(Of MeasFilterEntry)
                .Segmentation.FilterRanges.Add( New MeasFilterEntry(eMeasures.RgnArea,0R,10000000R))
            .Run(doc1)
        End With

        'Set APPLY FILTERS to OFF

        With Measure.MeasurementsCommands.Options(Nothing)
            .Segmentation.ApplyFilters = False
            .Run(doc1)
        End With

        'Learn OBJECT COUNT

        With measure.MeasurementsCommands.GetData(Nothing)
            .Run(ThisApplication.ActiveDocument, MyData)
        End With

        MyObjectCount = MyData.Statistics(eMeasures.RgnArea).count

        'Learn CALIBRATION INFORMATION

        If (ThisApplication.ActiveImage.SpatialCalibration IsNot Nothing) _
            Then

                MyCalibrationUnits = _
                    ThisApplication.ActiveImage.SpatialCalibration.UnitAbbrev

                MyPixelSizeX = _
                    ThisApplication.ActiveImage.SpatialCalibration.PixelSizeX

                MyPixelSizeY = _
                    ThisApplication.ActiveImage.SpatialCalibration.PixelSizeY

            Else

                MyCalibrationUnits = _
                    "pix"

                MyPixelSizeX = _
                    1

                MyPixelSizeY = _
                    1

            End If

        'Learn AOI AREA

        If (ThisApplication.ActiveImage.Aoi.Count > 0) _
            Then

                MyRoiArea = _
                    ThisApplication.ActiveImage.Aoi.mRgnArea.Sum

            Else

                MyRoiArea = _
                    ( ThisApplication.ActiveImage.Width * MyPixelSizeX ) * _
                    ( ThisApplication.ActiveImage.Height * MyPixelSizeY )

            End If

        'Calculate OBJECT DENSITY

        MyObjectDensity = MyObjectCount / MyRoiArea

        'Create RESULTS STRING

        MyResults = _
            "COUNT = " & vbTab & MyObjectCount & vbTab & "(units)" & vbLf & _
            "ROI AREA = " & vbTab & MyRoiArea & vbTab & "(" & MyCalibrationUnits & "^2)" & vbLf & _
            "DENSITY = " & vbTab & MyObjectDensity & vbTab & "(per " & MyCalibrationUnits & ")" & vbLf & _
            ""

        'Display RESULTS STRING in OUTPUT WINDOW

        ThisApplication.Output.show
        ThisApplication.Output.Clear
        ThisApplication.Output.PrintMessage(MyResults)

        'Send RESULTS STRING to CLIPBOARD

        system.Windows.Clipboard.SetText (MyResults)

    End Function

End Module

 

PaulSheppard

many thanks for this - I'll give it a try