Analyzing diffraction pattern with ImageJ

In summary, the conversation is about using ImageJ to analyze diffraction patterns from TEM and how to calculate the lattice parameter by obtaining Miller Indices from recognizable planes in the picture, electron wavelength, and camera length. The instructions state that the camera length can be obtained by using "Ctrl+I" in ImageJ and the file's description should contain this information. The conversation also includes information read from the dm3 file, such as the image size, resolution, and calibration function. The person asking the question is looking for help in obtaining the camera length and is asking for information from someone who may have had a similar problem.
  • #1
Mikhail_MR
17
0
Hey!

I have a very unusual question. It is about using ImageJ to analyze diffraction patterns from TEM.

1. Homework Statement
To calculate lattice parameter I need Miller Indices from planes I can recognize in the picture, wavelength of electrons and camera length. In our instructions for this experiment stays that I can get camera length using "Ctrl+I" in ImageJ. File's description should contain this information.

2. Information readed from the dm3 file
root.ApplicationBounds = {0,0,935,1280}
root.DocumentObjectList.0.AnnotationGroupList.0.AnnotationType = 12
root.DocumentObjectList.0.AnnotationGroupList.0.BackgroundColor = {-1,-1,-1}
root.DocumentObjectList.0.AnnotationGroupList.0.BackgroundMode = 1
root.DocumentObjectList.0.AnnotationGroupList.0.FillMode = 2
root.DocumentObjectList.0.AnnotationGroupList.0.ForegroundColor = {0,0,0}
root.DocumentObjectList.0.AnnotationGroupList.0.HasBackground = true
root.DocumentObjectList.0.AnnotationGroupList.0.IntegrationWidth = 1
root.DocumentObjectList.0.AnnotationGroupList.0.IsMoveable = true
root.DocumentObjectList.0.AnnotationGroupList.0.IsResizable = true
root.DocumentObjectList.0.AnnotationGroupList.0.IsSelectable = true
root.DocumentObjectList.0.AnnotationGroupList.0.IsTranslatable = true
root.DocumentObjectList.0.AnnotationGroupList.0.IsVisible = true
root.DocumentObjectList.0.AnnotationGroupList.0.Rectangle = {264.0,447.0,264.0,447.0}
root.DocumentObjectList.0.AnnotationGroupList.0.UniqueID = 2
root.DocumentObjectList.0.AnnotationType = 20
root.DocumentObjectList.0.BackgroundColor = {-1,-1,-1}
root.DocumentObjectList.0.BackgroundMode = 1
root.DocumentObjectList.0.FillMode = 1
root.DocumentObjectList.0.ForegroundColor = {0,0,0}
root.DocumentObjectList.0.HasBackground = true
root.DocumentObjectList.0.ImageDisplayInfo.BrightColor = {-1,-1,-1}
root.DocumentObjectList.0.ImageDisplayInfo.Brightness = 0.5
root.DocumentObjectList.0.ImageDisplayInfo.CaptionOn = false
root.DocumentObjectList.0.ImageDisplayInfo.CLUT.Size = 1536
root.DocumentObjectList.0.ImageDisplayInfo.CLUT.Offset = 1186
root.DocumentObjectList.0.ImageDisplayInfo.CLUTName = Greyscale
root.DocumentObjectList.0.ImageDisplayInfo.ComplexMode = 4
root.DocumentObjectList.0.ImageDisplayInfo.ComplexRange = 1000.0
root.DocumentObjectList.0.ImageDisplayInfo.Contrast = 0.5
root.DocumentObjectList.0.ImageDisplayInfo.ContrastMode = 1
root.DocumentObjectList.0.ImageDisplayInfo.DoAutoSurvey = true
root.DocumentObjectList.0.ImageDisplayInfo.EstimatedMax = -11.0
root.DocumentObjectList.0.ImageDisplayInfo.EstimatedMaxTrimPercentage = 0.0010
root.DocumentObjectList.0.ImageDisplayInfo.EstimatedMin = 241.0
root.DocumentObjectList.0.ImageDisplayInfo.EstimatedMinTrimPercentage = 0.0010
root.DocumentObjectList.0.ImageDisplayInfo.Gamma = 0.5
root.DocumentObjectList.0.ImageDisplayInfo.HighLimit = 400.0
root.DocumentObjectList.0.ImageDisplayInfo.HiLimitContrastDeltaTriggerPercentage = 0.0
root.DocumentObjectList.0.ImageDisplayInfo.IsInverted = false
root.DocumentObjectList.0.ImageDisplayInfo.LowLimit = -24.0
root.DocumentObjectList.0.ImageDisplayInfo.LowLimitContrastDeltaTriggerPercentage = 0.0
root.DocumentObjectList.0.ImageDisplayInfo.MainSliceId.0 = 0
root.DocumentObjectList.0.ImageDisplayInfo.MinimumContrast = 50.0
root.DocumentObjectList.0.ImageDisplayInfo.RangeAdjust = 1.0
root.DocumentObjectList.0.ImageDisplayInfo.SparseSurvey_GridSize = 16
root.DocumentObjectList.0.ImageDisplayInfo.SparseSurvey_NumberPixels = 32
root.DocumentObjectList.0.ImageDisplayInfo.SparseSurvey_UseNumberPixels = true
root.DocumentObjectList.0.ImageDisplayInfo.SurveyTechique = 0
root.DocumentObjectList.0.ImageDisplayType = 1
root.DocumentObjectList.0.ImageSource = 0
root.DocumentObjectList.0.IsMoveable = true
root.DocumentObjectList.0.IsResizable = true
root.DocumentObjectList.0.IsSelectable = true
root.DocumentObjectList.0.IsTranslatable = true
root.DocumentObjectList.0.IsVisible = true
root.DocumentObjectList.0.ObjectTags.__is_not_copy = true
root.DocumentObjectList.0.ObjectTags.__last_click_time = 9541690
root.DocumentObjectList.0.ObjectTags.__was_selected = false
root.DocumentObjectList.0.Rectangle = {0.0,0.0,512.0,512.0}
root.DocumentObjectList.0.UniqueID = 1
root.HasWindowPosition = true
root.Image Behavior.DoIntegralZoom = true
root.Image Behavior.ImageDisplayBounds = {0.0,0.0,512.0,512.0}
root.Image Behavior.IsZoomedToWindow = true
root.Image Behavior.UnscaledTransform.Offset = {0.0,0.0}
root.Image Behavior.UnscaledTransform.Scale = {1.0,1.0}
root.Image Behavior.ViewDisplayID = 1
root.Image Behavior.WindowRect = {0.0,0.0,682.0,682.0}
root.Image Behavior.ZoomAndMoveTransform.Offset = {85.0,85.0}
root.Image Behavior.ZoomAndMoveTransform.Scale = {1.0,1.0}
root.ImageList.0.ImageData.Calibrations.Brightness.Origin = 0.0
root.ImageList.0.ImageData.Calibrations.Brightness.Scale = 1.0
root.ImageList.0.ImageData.Calibrations.Dimension.0.Origin = 0.0
root.ImageList.0.ImageData.Calibrations.Dimension.0.Scale = 1.0
root.ImageList.0.ImageData.Calibrations.Dimension.1.Origin = 0.0
root.ImageList.0.ImageData.Calibrations.Dimension.1.Scale = 1.0
root.ImageList.0.ImageData.Calibrations.DisplayCalibratedUnits = true
root.ImageList.0.ImageData.Data.Size = 147456
root.ImageList.0.ImageData.Data.Offset = 5044
root.ImageList.0.ImageData.DataType = 23
root.ImageList.0.ImageData.Dimensions.0 = 192
root.ImageList.0.ImageData.Dimensions.1 = 192
root.ImageList.0.ImageData.PixelDepth = 4
root.ImageList.0.Name = Image Of GaAs_DP for students
root.ImageList.0.UniqueID.0 = 374618129
root.ImageList.0.UniqueID.1 = 914712398
root.ImageList.0.UniqueID.2 = 1097477823
root.ImageList.0.UniqueID.3 = 765151021
root.ImageList.1.ImageData.Calibrations.Brightness.Origin = 0.0
root.ImageList.1.ImageData.Calibrations.Brightness.Scale = 1.0
root.ImageList.1.ImageData.Calibrations.Dimension.0.Origin = 0.0
root.ImageList.1.ImageData.Calibrations.Dimension.0.Scale = 0.040000003
root.ImageList.1.ImageData.Calibrations.Dimension.0.Units = µm
root.ImageList.1.ImageData.Calibrations.Dimension.1.Origin = 0.0
root.ImageList.1.ImageData.Calibrations.Dimension.1.Scale = 0.040000003
root.ImageList.1.ImageData.Calibrations.Dimension.1.Units = µm
root.ImageList.1.ImageData.Calibrations.DisplayCalibratedUnits = true
root.ImageList.1.ImageData.Data.Size = 8388608
root.ImageList.1.ImageData.Data.Offset = 153216
root.ImageList.1.ImageData.DataType = 1
root.ImageList.1.ImageData.Dimensions.0 = 2048
root.ImageList.1.ImageData.Dimensions.1 = 2048
root.ImageList.1.ImageData.PixelDepth = 2
root.ImageList.1.ImageTags.Acquisition Mode = Gain Normalized
root.ImageList.1.ImageTags.CCD Size = 2048 x 2048
root.ImageList.1.ImageTags.DataBar.Acquisition Date = 20.11.08
root.ImageList.1.ImageTags.DataBar.Acquisition Time = 11:04:10
root.ImageList.1.ImageTags.DataBar.Exposure Number = 158988
root.ImageList.1.ImageTags.Microscope Info.AskedForMagnificationYet = false
root.ImageList.1.ImageTags.Microscope Info.AskForMagnificationMethod = 2
root.ImageList.1.ImageTags.Microscope Info.Cs(mm) = 0.6
root.ImageList.1.ImageTags.Microscope Info.Indicated Magnification = 600.0
root.ImageList.1.ImageTags.Microscope Info.Name = JEM3010
root.ImageList.1.ImageTags.Microscope Info.Voltage = 300000.0
root.ImageList.1.ImageTags.MSC.Alternate Shutter = 0
root.ImageList.1.ImageTags.MSC.Antiblooming = 1
root.ImageList.1.ImageTags.MSC.Area = {0,0,2048,2048}
root.ImageList.1.ImageTags.MSC.Binning = 1
root.ImageList.1.ImageTags.MSC.Camera Number = 0
root.ImageList.1.ImageTags.MSC.Exposure = 0.05
root.ImageList.1.ImageTags.MSC.Mode = 3.0
root.ImageList.1.ImageTags.MSC.Normally Closed = 1
root.ImageList.1.ImageTags.MSC.Physical Pixel Size = 24.0
root.ImageList.1.ImageTags.MSC.Processing = 3.0
root.ImageList.1.ImageTags.MSC.Set = 2.0
root.ImageList.1.ImageTags.MSC.Settling = 1
root.ImageList.1.ImageTags.MSC.Zoom = 3.0
root.ImageList.1.ImageTags.Source = Gatan SSC
root.ImageList.1.Name = GaAs_DP for students
root.ImageList.1.UniqueID.0 = 17204
root.ImageList.1.UniqueID.1 = 31898
root.ImageList.1.UniqueID.2 = 5829
root.ImageList.1.UniqueID.3 = 7839
root.ImageSourceList.0.ClassName = ImageSource:Simple
root.ImageSourceList.0.Id.0 = 0
root.ImageSourceList.0.ImageRef = 1
root.InImageMode = true
root.MinVersionList.0.RequiredVersion = 50659328
root.NextDocumentObjectID = 25
root.Page Behavior.DoIntegralZoom = false
root.Page Behavior.IsZoomedToWindow = true
root.Page Behavior.LayedOut = false
root.Page Behavior.PageTransform.Offset = {0.0,0.0}
root.Page Behavior.PageTransform.Scale = {1.0,1.0}
root.Page Behavior.RestoreImageDisplayBounds = {0.0,0.0,2048.0,2048.0}
root.Page Behavior.RestoreImageDisplayID = 1
root.Page Behavior.TargetDisplayID = -1
root.PageSetup.General = {1,268435556,21000,29700,2500,2500,-2500,-2500}
root.PageSetup.Win32.Size = 60
root.PageSetup.Win32.Offset = 8544055
root.PageSetup.Win32_DevModeW.Size = 8120
root.PageSetup.Win32_DevModeW.Offset = 8544152
root.PageSetup.Win32_DevNamesW.Size = 166
root.PageSetup.Win32_DevNamesW.Offset = 8552310
root.Thumbnails.0.ImageIndex = 0
root.Thumbnails.0.SourceSize_Pixels = {512,512}
root.WindowPosition = {121,242,803,924}

------------------------------------------------------
ImageJ 1.49v; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 40MB of 6057MB (<1%)

Title: GaAs_DP_60cm_ for students.dm3
Width: 81.9200 microns (2048)
Height: 81.9200 microns (2048)
Size: 8MB
Resolution: 25.0000 pixels per micron
Pixel size: 0.0400x0.0400 micron^2
ID: -18
Bits per pixel: 16 (signed)
Display range: -24 - 400
No threshold
Magnification: 0.25

Calibration function: y = a+bx
a: -32768.000000
b: 1.000000
Unit: "Gray Value"
Path: C:\Users\Mikhail\Desktop\Daten\P01\GaAs_DP_60cm_ for students.dm3
Screen location: 12,107 (1366x768)
No overlay

No selectionHow I can get camera length from this?

With best regards
Mikhail
 
  • #3
hey,

Did you get the answer for this?
I'm currently got the same problem as you.
Could you please provide the information on how to get the camera length?
'
Best regards
 

1. What is ImageJ and how is it used in diffraction pattern analysis?

ImageJ is a free, open-source software used for image processing and analysis. It is commonly used in scientific research, including the analysis of diffraction patterns. ImageJ allows for the measurement and quantification of various features in an image, such as the intensity and spacing of diffraction peaks.

2. How do I import my diffraction pattern into ImageJ?

To import your diffraction pattern into ImageJ, open the software and go to File > Open. Select your image file and it will be imported into ImageJ for analysis. You can also drag and drop the image file directly into the ImageJ window.

3. Can ImageJ be used to identify and measure diffraction peaks?

Yes, ImageJ has tools that allow for the identification and measurement of diffraction peaks. The “Find Peaks” function can automatically locate and mark the peaks in your diffraction pattern, and the “Measure” function can provide quantitative data such as peak intensity and distance between peaks.

4. How can I analyze the spacing between diffraction peaks using ImageJ?

To analyze the spacing between diffraction peaks in ImageJ, you can use the “Straight Line” tool to draw a line between two peaks. Then, go to Analyze > Measure to obtain the length of the line. This can be used to calculate the spacing between the peaks.

5. Are there any plugins or extensions for ImageJ that can assist in diffraction pattern analysis?

Yes, there are several plugins and extensions available for ImageJ that can assist in diffraction pattern analysis. Some examples include the “DiffractionLab” plugin, which allows for the simulation and modeling of diffraction patterns, and the “Diffraction Analyzer” plugin, which can automatically detect and analyze diffraction peaks.

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