Analyzing diffraction pattern with ImageJ

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SUMMARY

The discussion focuses on using ImageJ 1.49v to analyze diffraction patterns from Transmission Electron Microscopy (TEM) images, specifically for calculating lattice parameters using Miller Indices. Users can obtain the camera length by pressing "Ctrl+I" in ImageJ, which reveals necessary file information. The discussion highlights the importance of understanding the metadata from the .dm3 file format, including pixel size and calibration functions, to accurately interpret diffraction patterns.

PREREQUISITES
  • Familiarity with ImageJ 1.49v
  • Understanding of Transmission Electron Microscopy (TEM) principles
  • Knowledge of Miller Indices and lattice parameters
  • Basic skills in interpreting .dm3 file metadata
NEXT STEPS
  • Research how to extract and interpret metadata from .dm3 files in ImageJ
  • Learn about Miller Indices and their application in crystallography
  • Explore advanced features of ImageJ for image analysis in TEM
  • Investigate calibration techniques for accurate measurements in microscopy
USEFUL FOR

This discussion is beneficial for researchers, students, and professionals in materials science and microscopy who are analyzing diffraction patterns and require precise measurements from TEM images.

Mikhail_MR
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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
 
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
 

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