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Laboratory Instruments

Here we report the meta data files generated by different laboratory microCT instruments.

Bruker

SkyScan 1173

SkyScan 1173 instruments generates the following meta-data files:

  1. :download:`sample_name.log <../demo/bruker/skyscan_1173/MML0514A_gg_lumbar1_al_26.8um_2k_.log>`

meta-data

[System]

Scanner SkyScan1173
Instrument S/N 18O05071
Hardware version A
Software Version 1. 6 (build 22)
Home directory C:SkyScan1173
Source Type Hamamatsu 130/300
Camera FlatPanel Sensor
Camera Pixel Size (um) 50.0
CameraXYRatio 1.0740
Incl.in lifting (um/mm) 0.1930

[Acquisition]

Data directory E:resultsLab filesJamiecetacean scansMML0514A_gg_lumbar1_al_26.8um_2k_
Filename Prefix MML0514A_gg_lumbar1_al_26.8um_2k_
Number of Files 1200
Source Voltage (kV) 120
Source Current (uA) 60
Number of Rows 2240
Number of Columns 2240
Image crop origin X 0
Image crop origin Y 0
Camera binning 1x1
Image Rotation 0.1700
Gantry direction CC
Number of connected scans 1
Image Pixel Size (um) 26.844857
Scaled Image Pixel Size (um) 26.844857
Object to Source (mm) 197.738
Camera to Source (mm) 364.000
Vertical Object Position (mm) 2.000
Optical Axis (line) 1088
Filter Al 1.0mm
Image Format TIFF
Depth (bits) 16
Screen LUT 0
Exposure (ms) 700
Rotation Step (deg) 0.200
Frame Averaging ON (3)
Random Movement ON (4)
Use 360 Rotation NO
Partial width 100
FF updating interval 201
Geometrical Correction OFF
Camera Offset OFF
Median Filtering OFF
Flat Field Correction ON
Rotation Direction CC
Scanning Trajectory ROUND
Type Of Motion STEP AND SHOOT
Study Date and Time Jul 20, 2023 11:26:30
Scan duration 01:11:47
Maximum vertical TS 1.0
Maximum horizontal TS 0.0
TS modified at July20,12:15:07 --- 1200 of 1200 projections
TS modified according to E:resultsLab filesJamiecetacean scansMML0514A_gg_lumbar1_al_26.8um_2k_MML0514A_gg_lumbar1_al_26.8um_2k__TS.csv
TS modified at level 0

[Reconstruction]

Reconstruction Program NRecon
Program Version Version: 1.7.1.0
Program Home Directory C:SkyScan1173
Reconstruction engine GPUReconServer
Engine version Version: 1.7.1
Reconstruction from batch No
Postalignment 0.50
Reconstruction servers SKYSCAN1173
Dataset Origin SkyScan1173
Dataset Prefix MML0514A_gg_lumbar1_al_26.8um_2k_
Dataset Directory E:resultsLab filesJamiecetacean scansMML0514A_gg_lumbar1_al_26.8um_2k_
Output Directory E:resultsLab filesJamiecetacean scansMML0514A_gg_lumbar1_al_26.8um_2k_MML0514A_gg_lumbar1_al_26.8um_2k_Rec
Time and Date Jul 20, 2023 12:35:34
First Section 379
Last Section 2219
Reconstruction duration per slice (seconds) 0.477458
Total reconstruction time (1841 slices) in seconds 879.000000
Section to Section Step 1
Sections Count 1841
Result File Type BMP
Result File Header Length (bytes) 1134
Result Image Width (pixels) 2240
Result Image Height (pixels) 2240
Pixel Size (um) 26.84486
Reconstruction Angular Range (deg) 240.00
Use 180+ OFF
Angular Step (deg) 0.2000
Smoothing 0
Ring Artifact Correction 9
Draw Scales OFF
Object Bigger than FOV OFF
Reconstruction from ROI OFF
Filter cutoff relative to Nyquist frequency 100
Filter type 0
Filter type description Hamming (Alpha=0.54)
Undersampling factor 1
Threshold for defect pixel mask (%) 0
Beam Hardening Correction (%) 15
CS Static Rotation (deg) 0.00
Minimum for CS to Image Conversion 0.000000
Maximum for CS to Image Conversion 0.016200
HU Calibration OFF
BMP LUT 0
Cone-beam Angle Horiz.(deg) 17.291304
Cone-beam Angle Vert.(deg) 17.291304

SkyScan 1272

SkyScan 1272 instruments generates the following meta-data files:

  1. :download:`sample_name.log <../demo/bruker/skyscan_1272/DRP_P21_3/DRP_P21_3.log>`

meta-data

[System]

Scanner SkyScan1272
Instrument S/N 19N09230
Software Version 1.4
Home Directory C:\SkyScan1272
Source Type HAMAMATSU_L10101-67
Camera Type XIMEA xiRAY11
Camera Pixel Size (um) 9.0
Camera X/Y Ratio 0.9851

[User]

User Name Skyscan
Computer Name SCAN1272-230

[Acquisition]

Data Directory D:\Results\2023_03_14 P21_3
Filename Prefix DRP_P21_3~00
Filename Index Length 8
Number Of Files 471
Number Of Rows 896
Number Of Columns 1075
Partial Width 80%
Image crop origin X 134
Image crop origin Y 0
Camera binning 3x3
Image Rotation 0.05700
Optical Axis (line) 528
Camera to Source (mm) 270.98833
Object to Source (mm) 200.70900
Source Voltage (kV) 60
Source Current (uA) 166
Image Pixel Size (um) 19.797722
Scaled Image Pixel Size (um) 19.797722
Image Format TIFF
Depth (bits) 16
Reference Intensity 57000
Camera position Far
Exposure (ms) 1175
Rotation Step (deg) 0.400
Use 360 Rotation NO
Scanning position 28.344 mm
Frame Averaging ON (3)
Random Movement ON (20)
Flat Field Correction ON
FF updating interval 68
Geometrical Correction ON
Filter Al 0.25mm
Gantry direction CC
Rotation Direction CC
Type of Detector Motion STEP AND SHOOT
Scanning Trajectory ROUND
Beam position 0
Skip extra frame On
Source spot size Small
Number Of Horizontal Offset Positions 1
Number of connected scans 2
Current scan number 1
Number of lines to be reconstructed 578
Study Date and Time 14 Mar 2023 09h:00m:40s
Scan duration 0h:54m:2s
Maximum vertical TS 5.0

[Reconstruction]

Reconstruction Program NRecon
Program Version Version: 2.0.0.5
Program Home Directory C:\SkyScan1272
Reconstruction engine GPUReconServer
Engine version Version: 2.0.0
Reconstruction from batch No
Postalignment Applied 1
Reconstructed using oversize option=Yes
Connected Reconstruction (parts) 2
Sub-scan post alignment [0] 0.000000
Sub-scan post alignment [1] 1.500000
Sub-scan scan length [0] 573
Sub-scan scan length [1] 578
Used extra rotation per scan(deg) 0.000 0.000
Used extra shift in X per scan(micron) 0.000 -2.152
Used extra shift in Y per scan(micron) 0.000 4.272
Reconstruction servers SCAN1272-230
Dataset Origin SkyScan1272
Dataset Prefix DRP_P21_3~00
Dataset Directory D:\Results\2023_03_14 P21_3
Output Directory D:\Results\2023_03_14 P21_3\DRP_P21_3_Rec
Time and Date 14 Mar 2023 10h:02m:54s
First Section 27
Last Section 1454
Reconstruction duration per slice (seconds) 0.016497
Total reconstruction time (788 slices) in seconds 13.000000
Section to Section Step 1
Sections Count 1428
Result File Type BMP
Result File Header Length (bytes) 1134
Result Image Width (pixels) 944
Result Image Height (pixels) 944
Pixel Size (um) 19.79772
Reconstruction Angular Range (deg) 188.40
Use 180+ OFF
Angular Step (deg) 0.4000
Smoothing 1
Smoothing kernel 0 (Asymmetrical boxcar)
Ring Artifact Correction 5
Draw Scales OFF
Object Bigger than FOV OFF
Reconstruction from ROI ON_ROUND
ROI Top (pixels) 1012
ROI Bottom (pixels) 65
ROI Left (pixels) 125
ROI Right (pixels) 1072
ROI reference length 1075
Filter cutoff relative to Nyquist frequency 100
Filter type 0
Filter type description Hamming (Alpha=0.54)
Undersampling factor 1
Threshold for defect pixel mask (%) 0
Beam Hardening Correction (%) 10
CS Static Rotation (deg) 0.00
CS Static Rotation Total(deg) 0.00
Minimum for CS to Image Conversion 0.000000
Maximum for CS to Image Conversion 0.136673
HU Calibration OFF
BMP LUT 0
Cone-beam Angle Horiz.(deg) 6.069781
Cone-beam Angle Vert.(deg) 5.060536
  1. :download:`sample_name_Rec\\sample_name_rec.log <../demo/bruker/skyscan_1272/DRP_P21_3/DRP_P21_3_Rec/DRP_P21_3_rec.log>`

[System]

Scanner SkyScan1272
Instrument S/N 19N09230
Software Version 1.4
Home Directory C:\SkyScan1272
Source Type HAMAMATSU_L10101-67
Camera Type XIMEA xiRAY11
Camera Pixel Size (um) 9.0
Camera X/Y Ratio 0.9851

[User]

User Name Skyscan
Computer Name SCAN1272-230

[Acquisition]

Data Directory D:\Results\2023_03_14 P21_3
Filename Prefix DRP_P21_3~00
Filename Index Length 8
Number Of Files 471
Number Of Rows 896
Number Of Columns 1075
Partial Width 80%
Image crop origin X 134
Image crop origin Y 0
Camera binning 3x3
Image Rotation 0.05700
Optical Axis (line) 528
Camera to Source (mm) 270.98833
Object to Source (mm) 200.70900
Source Voltage (kV) 60
Source Current (uA) 166
Image Pixel Size (um) 19.797722
Scaled Image Pixel Size (um) 19.797722
Image Format TIFF
Depth (bits) 16
Reference Intensity 57000
Camera position Far
Exposure (ms) 1175
Rotation Step (deg) 0.400
Use 360 Rotation NO
Scanning position 28.344 mm
Frame Averaging ON (3)
Random Movement ON (20)
Flat Field Correction ON
FF updating interval 68
Geometrical Correction ON
Filter Al 0.25mm
Gantry direction CC
Rotation Direction CC
Type of Detector Motion STEP AND SHOOT
Scanning Trajectory ROUND
Beam position 0
Skip extra frame On
Source spot size Small
Number Of Horizontal Offset Positions 1
Number of connected scans 2
Current scan number 1
Number of lines to be reconstructed 578
Study Date and Time 14 Mar 2023 09h:00m:40s
Scan duration 0h:54m:2s
Maximum vertical TS 5.0

[Reconstruction]

Reconstruction Program NRecon
Program Version Version: 2.0.0.5
Program Home Directory C:SkyScan1272
Reconstruction engine GPUReconServer
Engine version Version: 2.0.0
Reconstruction from batch No
Postalignment Applied 1
Reconstructed using oversize-option Yes
Connected Reconstruction (parts) 2
Sub-scan post alignment [0] 0.000000
Sub-scan post alignment [1] 1.500000
Sub-scan scan length [0] 573
Sub-scan scan length [1] 578
Used extra rotation per scan(deg) 0.000 0.000
Used extra shift in X per scan(micron) 0.000 -2.152
Used extra shift in Y per scan(micron) 0.000 4.272
Reconstruction servers SCAN1272-230
Dataset Origin SkyScan1272
Dataset Prefix DRP_P21_3~00
Dataset Directory D:\Results\2023_03_14 P21_3
Output Directory D:\Results\2023_03_14 P21_3\DRP_P21_3_Rec
Time and Date 14 Mar 2023 10h:02m:54s
First Section 27
Last Section 1454
Reconstruction duration per slice (seconds) 0.016497
Total reconstruction time (788 slices) in seconds 13.000000
Section to Section Step 1
Sections Count 1428
Result File Type BMP
Result File Header Length (bytes) 1134
Result Image Width (pixels) 944
Result Image Height (pixels) 944
Pixel Size (um) 19.79772
Reconstruction Angular Range (deg) 188.40
Use 180+ OFF
Angular Step (deg) 0.4000
Smoothing 1
Smoothing kernel 0 (Asymmetrical boxcar)
Ring Artifact Correction 5
Draw Scales OFF
Object Bigger than FOV OFF
Reconstruction from ROI ON_ROUND
ROI Top (pixels) 1012
ROI Bottom (pixels) 65
ROI Left (pixels) 125
ROI Right (pixels) 1072
ROI reference length 1075
Filter cutoff relative to Nyquist frequency 100
Filter type 0
Filter type description Hamming (Alpha=0.54)
Undersampling factor 1
Threshold for defect pixel mask (%) 0
Beam Hardening Correction (%) 10
CS Static Rotation (deg) 0.00
CS Static Rotation Total(deg) 0.00
Minimum for CS to Image Conversion 0.000000
Maximum for CS to Image Conversion 0.136673
HU Calibration OFF
BMP LUT 0
Cone-beam Angle Horiz.(deg) 6.069781
Cone-beam Angle Vert.(deg) 5.060536
Sub-Scan 0 ends at slice 814
Sub-Scan 1 ends at slice 1449
Automatic matching in Z 50
Automatic matching in X/Y 50
Automatic matching in rotation 5.000000
Automatic fusion 0

[File name convention]

Filename Index Length 8
Filename Prefix DRP_P21_3_rec

G E

GE Phoenix instruments generates the following meta-data files:

  1. :download:`sample_name.dtxml <../demo/ge/FEG230530_409-run-files/FEG230530_409.dtxml>`

meta-data

Operator Goetz, Freya
Researcher  
NMNH PI Osborn, KaREn
Department Invertebrate Zoology
Project Name  
Project Number  
Sample ID usnm1615674
Sample Description. PTA+EtOH
Sample Name Euphausia hemigibba
Sample Type  
  1. :download:`sample_name.pca <../demo/ge/FEG230530_409-run-files/FEG230530_409.pca>`

[General]

Version 2.4.0.1843
Version-pca 2
Comment  
LoadDefault 1
SystemName National Museum of Natural History GE Phoenix v tome x m µCT

[AutoScO]

Active 1
ImgNr 8
ImageString 162:324:486:648:810:972:1134:1300
Skip 10

[Geometry]

FDD 807.13534640
FOD 41.52975000
Magnification 19.43511209
VoxelSizeX 0.01029065
VoxelSizeY 0.01029065
CalibValue 28.524
cx 1006.50000000
cy 1011.50000000
DetectorRot 0.00000000
Tilt 0.00000000
Old_CalibValue 0.00000000

[CT]

Type 0
NumberImages 1300
StartImg 1301
RotationSector 360.00000000
NoRotation 0
EstimatedTime 0
RemainingTime 1300
ScanTimeCmpl 1300
NrImgDone 1301
NrImgCmplScan 1301
RefDriveEnabled 0
SkipForNewInterval 25
SkipAcc 1
FreeRayFactor 1.00010000
Wnd_L 0
Wnd_T 0
Wnd_R 10
Wnd_B 10
Level 3123.00000000

[VSensor]

EnableTiles 1
Start 0
NumTiles 1
Interval 60
Overlap 9
AdjustImg 1
SingleImgX 2024

[Trajectory]

Active 0

[CalibValue]

NumberImages 18
Averaging 2
Skip 3

[FastCT]

Active 0

[Image]

Top 0
Left 0
Bottom 2023
Right 2023
DimX 2014
DimY 2024
Rotation 0
FreeRay 3250

[ImgProc]

SwBin 1
AddSwBin 0

[Warmup]

Enable 1
Counter 0
MaxTimes 10
TimeTrigOn 0
kV 95
Time 60

[Multiscan]

Active 0

[Multiline]

Installed 0

[CalibImages]

MGainPoints 2
Avg 100
Skip 10
EnableAutoAcq 1
MGainVoltage 90:90:
MGainCurrent 30:110:
GainImg S:\CT_DATA\Invertebrate Zoology\Goetz, Freya\FEG230530_409\FEG230530_409_bright_90kV_110uA_500ms_1Det.tif
MGainImg S:\CT_DATA\Invertebrate Zoology\Goetz, Freya\FEG230530_409\FEG230530_409_bright_90kV_110uA_500ms_1Det.tif
OffsetImg S:\CT_DATAInvertebrate Zoology\Goetz, Freya\FEG230530_409\FEG230530_409_Dark_500.tif
DefPixelImg C:\Program Files\phoenix x-ray\datosx 2 acq\CalibrationImages\pixmask_B1x1_x2024_y2024.tif

[SectorScan]

Active 0

[DetectorShift]

Enable 1
Mode 0
Amplitude 5
Interval 1
Step 1

[Detector]

InitTimeOut 60000
Name dxr-250
PixelsizeX 0.20000000
PixelsizeY 0.20000000
NrPixelsX 2024
NrPixelsY 2024
Timing 4
TimingVal 500.102
Avg 3
Skip 1
Binning 0
BitPP 16
CameraGain 2
SatValue 15563
SatPixNrLimit 4096

[Xray]

ComPort 0
Name xs 240 d
ID 2682
InitTimeout 20000
Voltage 90
Current 110
Mode 0
Filter Unknown
Collimation -1
WaitTime 1000
WaitForStable 30000
FocDistX 0.0000000
FocDistY 0.0000000
SpinStepkV 10
SpinStepuA 10
Macro 0
RestrictNumSpots 0
PreWarning 0
MinGainCurrent 10

[Cnc]

InitTimeout 8000
JoyDriveDoorOpen 0
SecPosSample 250.00000000
MinSampleDetPos 300.00000000
EnableKeyboardJoy 0
KeyJoyVelocityFactor 0.25000000

[CNC_0]

DtxName XS
LoadPos -149.999250
AcqPos 0.000000

[CNC_1]

DtxName YS
LoadPos 398.000000
AcqPos 232.685562

[CNC_2]

DtxName ZS
LoadPos 250.000188
AcqPos 41.529750

[CNC_3]

DtxName RS
LoadPos 1.646100
AcqPos 0.000000

[CNC_4]

DtxName XD
LoadPos 0.199750
AcqPos 0.000000

[Axis]

XSample 0.000000
YSample 232.685562
ZSample 41.529750
RSample 0.000000
XDetector 0.000000

[AcqSrvManager]

RecvPcIp  
ExePath c:\Program Files\phoenix x-ray\datosx 2 acq\srv\dtxaSrv.exe

[Net]

Enable 0
IP  

[BHC_Values]

BHC_Param 2
  1. :download:`sample_name.pcj <../demo/ge/FEG230530_409-run-files/FEG230530_409.pcj>`

[Info]

TrajectoryType 0
SystemType 20768
SystemName National Museum of Natural History GE Phoenix v|tome|x m µCT
NumImages 1300
NumSensors 1

[Data]

ImgNr XS YS ZS RS XD Warmup VSenCnt TimeStamp ChangeCnt
1 0.0000000 232.6855625 -41.5297500 0.0000000 -1.0000000 0 0 0 0
2 0.0000000 232.6855625 -41.5297500 0.2769231 0.2000000 0 0 0 0
3 0.0000000 232.6855625 -41.5297500 0.5538462 -0.6000000 0 0 0 0
4 0.0000000 232.6855625 -41.5297500 0.8307692 0.6000000 0 0 5554 0
  1. :download:`sample_name.pcp <../demo/ge/FEG230530_409-run-files/FEG230530_409.pcp>`

datos|x 2 acquisition 2.4.0

ImgNr RotPos U I MeanGV DevGV Dose Use CValue XDShift Time
1 0.000 90 109 3151.3 -0.9 0.0 1 0.000 -5 2023-05-30 09:58:20
2 0.277 90 109 3153.1 -0.9 0.0 1 0.000 1 2023-05-30 09:58:22
3 0.554 90 108 3152.6 -0.9 0.0 1 0.000 -3 2023-05-30 09:58:24
4 0.831 90 109 3159.1 -1.1 0.0 1 0.000 3 2023-05-30 09:58:26
  1. :download:`sample_name.pcr <../demo/ge/FEG230530_409-run-files/FEG230530_409.pcr>`

[Versions]

Version-PCR 2
Version-datos|x 2.4.0.1199 - RTM

[General]

ParameterSetOnly 0

[ImageData]

PCA_File S:\CT_DATA\Invertebrate Zoology\Goetz, Freya\FEG230530_409\FEG230530_409.pca

[ROI]

ROI_SizeX 456
ROI_SizeY 531
ROI_SizeZ 1951
ROI_OffX 97
ROI_OffY -273.5
ROI_OffZ 36.5

[Reconstruction Settings]

FreeRay 3250
UseFreeRayFromPCP 1
CorrectionValue 28.52400016784668
ObjectRotation 111.5999984741211
RecFilterKernel 2
ROI_Filter 1
StartImage 1
LastImage 1300
ImageFilter 0
VolumeFilter 0
VolumeGaussRadius 3
VolumeUSMContrast 50
VolumeUSMIterations 2
VolumeUSMRadius 3
VoxelOutlierPart 0

[VolumeData]

Volume_SizeX 456
Volume_SizeY 531
Volume_SizeZ 1951
VoxelSizeRec 0.0102906534448266
Resolution 1
Format 5
Min -0.0885586217045784
Max 3.274684190750122
VOL_File S:\CT_DATA\Invertebrate Zoology\Goetz, Freya\FEG230530_409\FEG230530_409.vol

[BHC_Values]

BHC_Param 2
ABC_Param_A 0
ABC_Param_B 0
ABC_Param_C 0
ABC_Param_D 0
ABC_Param_E 0
ABC_Param_F 0
ABC_Param_G 0
ABC_Param_H 0
ABC_Param_I 0
ABC_Param_J 0
ABC_Param_M 0
ABC_Threshold 0
ABC_RSquare 0
ABC_MaxThickness 100

[SCO_Values]

SCO_NumPoints 9
SCO_0_Index 162
SCO_0_Scale 1
SCO_0_X -0.2
SCO_0_Y -0
SCO_1_Index 324
SCO_1_Scale 1.0003
SCO_1_X 0.1
SCO_1_Y -0
SCO_2_Index 486
SCO_2_Scale 1.0007
SCO_2_X 0.5
SCO_2_Y -0
SCO_3_Index 648
SCO_3_Scale 1.0004
SCO_3_X 0.4
SCO_3_Y -0
SCO_4_Index 810
SCO_4_Scale 1.0003
SCO_4_X 0
SCO_4_Y 0
SCO_5_Index 972
SCO_5_Scale 1.0008
SCO_5_X -0.7
SCO_5_Y -0.2
SCO_6_Index 1134
SCO_6_Scale 1.0006
SCO_6_X -1.1
SCO_6_Y -0.1
SCO_7_Index 1300
SCO_7_Scale 1.0002
SCO_7_X -1
SCO_7_Y 0
SCO_8_Index 1301
SCO_8_Scale 1.0002
SCO_8_X -0.9
SCO_8_Y 0.1

[Metrology]

DetectorMaskUsed 0

Nikon

Nikon instruments create a folder using the sample name plus a space and the date-time as formatted below:

  • sample_name [2023-10-18 11.22.08]

Inside this folder the following meta data files are stored:

  1. :download:`_ctdata.txt <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/_ctdata.txt>`
  2. :download:`sample_name.xtekct <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/Lego_alignment test_1.xtekct>`
  3. :download:`sample_name_01.xtekct <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/Lego_alignment test_1_01.xtekct>`
  4. :download:`sample_name.ctinfo.xml <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/Lego_alignment test_1.ctinfo.xml>`
  5. :download:`sample_name.ctprofile.xml <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/Lego_alignment test_1.ctprofile.xml>`

_ctdata.txt

Contains the total number of Projections, the number of frames per projection and the exposure time in ms.

Projections Frames Exposure(ms)
1570 1 708.00

and the projection number, angle and time

Projection Angle(deg) Time(s)
1 000.0342 002.8319
2 000.2617 003.5397
3 000.4932 004.2479
4 000.7246 004.9576
5 000.9541 005.6639
6 001.1826 006.3739
7 001.4170 007.0800
8 001.6465 007.7898
9 001.8750 008.4961
10 002.1025 009.2044
11 002.3330 009.9126
12 002.5654 010.6203
13 002.7949 011.3283
14 003.0244 012.0368
15 003.2529 012.7444
16 003.4834 013.4524
17 003.7148 014.1607
18 003.9453 014.8685
19 004.1729 015.5768
'..' '......' '......'
1566 359.9180 1110.9320
1567 360.1504 1111.6410
1568 360.3799 1112.3480
1569 360.6094 1113.0560
1570 360.8379 1113.7640
1571 361.0664 1114.4720

:download:`_ctdata.txt <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/_ctdata.txt>`

sample_name.xtekct

sample_name.xtekct contains the following meta data:

CTPro

'anglefile_ignoreerrors' 'True'
'anglefile_use' 'False'
'autocor_numbands' '2'
'corautoaccuracy' '2'
'filter_material' 'Aluminium'
'filter_thicknessmm' '1.0'
'product' '[XT 5.4][Copyright (c) 2004-2019 Nikon Metrology NV]'
'shuttling' 'False'
'sliceheightmmdualbottom' '4.99999926'
'sliceheightmmdualtop' '14.99999779'
'sliceheightmmsingle' '9.99999853'
'version' 'V5.4.7289.18310 (Date:2019-12-16)'

DICOM

'dicomtags' '<?xml version="1.0" '
  'encoding="utf-16"?><ArrayOfMetaDataSchema '
  'xmlns:xsd="http://www.w3.org/2001/XMLSchema" '
  'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><MetaDataSchema '
  'xsi:type="MetaDataStringSchema"><Tag>Dataset '
  'name</Tag><Description>Dataset '
  'name</Description><Identifier>true</Identifier><DataValue>Lego_alignment '
  'test_1</DataValue><DicomTagGroup>0</DicomTagGroup><DicomTagElement>0</DicomTagElement></MetaDataSchema></ArrayOfMetaDataSchema>'

XTekCT

'angularstep' '0.2299575'
'automaticcentreofrotation' '0'
'autoscalingtype' '0'
'beamhardeninglutfile' ''
'blanking' '0'
'coefx0' '0.0'
'coefx1' '1.0'
'coefx2' '0.0'
'coefx3' '0.0'
'coefx4' '0.0'
'convolutionkernelsize' '0'
'cutofffrequency' '1.25'
'detectoroffsetx' '0.0'
'detectoroffsety' '0.0'
'detectorpixelsizex' '0.4'
'detectorpixelsizey' '0.4'
'detectorpixelsx' '1000'
'detectorpixelsy' '1000'
'exponent' '1.0'
'filtertype' '1'
'highpercentile' '99.8'
'importconversion' '1'
'increment' '1'
'initialangle' '40.20631'
'inputdigits' '4'
'inputfoldername' ''
'inputname' 'Lego_alignment test_1'
'inputseparator' '_'
'interpolationtype' '1'
'lowpercentile' '0.2'
'maskradius' '9.56649218'
'medianfilterkernelsize' '1'
'modifierid' ''
'name' 'Lego_alignment test_1'
'normalisation' '1.0'
'objectoffsetx' '-0.0277442'
'objectoffsety' '0.0'
'objectroll' '-0.07657059'
'objecttilt' '0.0'
'offsetx' '0.0'
'offsety' '0.0'
'offsetz' '-0.12043333'
'operatorid' ''
'orderfft' '12'
'outputdigits' '4'
'outputfoldername' 'Lego_alignment test_1'
'outputname' 'Lego_alignment test_1'
'outputseparator' '_'
'outputtype' '1'
'outputunits' '/m'
'projections' '1570'
'regionpixelsx' '1000'
'regionpixelsy' '1000'
'regionstartx' '0'
'regionstarty' '0'
'scale' '1.0'
'scaling' '1000.0'
'scalingmaximum' '1000.0'
'scalingminimum' '0.0'
'scattering' '0.0'
'srctodetector' '679.5143'
'srctoobject' '33.97571'
'srctovirtualdetector' '679.5143'
'units' 'mm'
'virtualdetectoroffsetx' '0.0'
'virtualdetectoroffsety' '0.0'
'virtualdetectorpixelsizex' '0.4'
'virtualdetectorpixelsizey' '0.4'
'virtualdetectorpixelsx' '1000'
'virtualdetectorpixelsy' '1000'
'voxelsizex' '0.02'
'voxelsizey' '0.02'
'voxelsizez' '0.02'
'voxelsx' '1000'
'voxelsy' '1000'
'voxelsz' '814'
'whitelevel' '58500'

Xrays

'xraykv' '90'
'xrayua' '32'

:download:`sample_name_01.xtekct <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/Lego_alignment test_1_01.xtekct>`

sample_name_01.xtekct

This is identical to the previous xtekct files.

:download:`sample_name_01.xtekct <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/Lego_alignment test_1_01.xtekct>`

sample_name.ctinfo.xml

'Information' '@xmlns:xsi' 'none'    
  'Elements' 'Element' 'tag' 'Dataset name
      'value' 'Lego_alignment test_1
  'Identifier' 'Lego_alignment test_1'    
  'JobGuid' 'b23b9e12-0c66-462a-a58f-ad43bafedd7e'    

:download:`sample_name.ctinfo.xml <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/Lego_alignment test_1.ctinfo.xml>`

sample_name.ctprofile.xml

{'CTProfile': {'@xmlns:xsi': 'none',
               'AutomaticallyPreprocess': 'true',
               'BeamHardeningLUTFile': None,
               'BeamHardeningPreset': '0',
               'CTAxisOffset': '0',
               'CalculateCentreOfRotation': 'false',
               'CoROffsetZ1': '0',
               'CoROffsetZ2': '0',
               'DataSetName': 'Lego_alignment test_1',
               'DatasetAcquisition': 'false',
               'Delay': {'Hours': '0', 'Minutes': '0', 'Seconds': '0'},
               'DetectorPixelSizeMM': '0.4',
               'DualCentreOfRotation': 'false',
               'FastPanelScan': 'false',
               'FluxNormalisation': 'false',
               'FluxNormalisationRect': {'Height': '100',
                                         'Location': {'X': '10', 'Y': '10'},
                                         'Size': {'Height': '100',
                                                  'Width': '100'},
                                         'Width': '100',
                                         'X': '10',
                                         'Y': '10'},
               'FramesPerProjection': '1',
               'HelicalScan': 'false',
               'ImagingSettings': {'@BlackToWhiteLatency': '0',
                                   '@WhiteToBlackLatency': '20000',
                                   '@WhiteToWhiteLatency': '1000',
                                   '@accumulation': '0',
                                   '@binning': '1',
                                   '@brightness': '0',
                                   '@digitalGain': '0',
                                   '@exposure': '708',
                                   '@gain': '3',
                                   '@lines': '1',
                                   'imageOffsetX': '24',
                                   'imageOffsetY': '24',
                                   'imageSizeX': '2000',
                                   'imageSizeY': '2000',
                                   'transform': '1'},
               'IntensifierField': '0',
               'IrisDemand': '100',
               'JobGuid': 'b23b9e12-0c66-462a-a58f-ad43bafedd7e',
               'LimitedAngleScan': 'false',
               'LinearInterpolation': 'true',
               'ManipulatorPosition': {'@Version': '2',
                                       'AxisPosition': ['1.00195634',
                                                        '497.5113',
                                                        '222.689911',
                                                        '324.7129',
                                                        '0']},
               'ManualCentreOfRotation': 'false',
               'MedianFilterSize': '1',
               'MetrologyMode': {'Apply': 'false',
                                 'CalibrationScan': 'false',
                                 'Reference': None,
                                 'ScanVOI': {'AdjustHeight': '0',
                                             'AdjustRadius': '0',
                                             'Height': '0'},
                                 'VolumeAnalysisMode': 'Automatic'},
               'MinimiseRingArtefacts': 'false',
               'NoiseReductionPreset': '0',
               'NumberOfDatasets': '1',
               'OptimiseProjections': 'true',
               'PanelScanImages': '1',
               'ProfileName': 'Lego_alignment test_1',
               'ProfileVersion': '0',
               'ProjectionImageEnhancement': 'None',
               'Projections': '1570',
               'Reconstruct': 'false',
               'ReconstructionOutput': {'AutoScalingType': '0',
                                        'FixedAttenuationHighInvMM': '1',
                                        'FixedAttenuationLowInvMM': '0',
                                        'ImportConversion': '0',
                                        'LinearAttenuationUnits': '2',
                                        'OutputDataFormat': '0',
                                        'PercentileHigh': '99.8',
                                        'PercentileLow': '0.2'},
               'ReconstructionPCName': 'JSXIR-CTLAB-REC',
               'ReconstructionQuality': '100',
               'SafeFocusDisabled': 'false',
               'SafePosition': {'@Version': '2',
                                'AxisPosition': ['57.40561',
                                                 '496.2577',
                                                 '222.689911',
                                                 '324.7129',
                                                 '0']},
               'ScanFlatPanel': 'false',
               'SelectVolumeAnalysis': 'NotSet',
               'ShadingCorrectionProfile': {'Frames': '43',
                                            'GreyLevelTargets': {'Target': [{'GreyLevel': '3939',
                                                                             'PercentageWhiteLevel': '0',
                                                                             'XrayFilterMaterial': None,
                                                                             'XrayFilterThickness': '0',
                                                                             'kV': '0',
                                                                             'uA': '0'},
                                                                            {'GreyLevel': '9871',
                                                                             'PercentageWhiteLevel': '100',
                                                                             'XrayFilterMaterial': 'Aluminium',
                                                                             'XrayFilterThickness': '1',
                                                                             'kV': '90',
                                                                             'uA': '32'}]},
                                            'ImagingConditions': {'@BlackToWhiteLatency': '0',
                                                                  '@WhiteToBlackLatency': '20000',
                                                                  '@WhiteToWhiteLatency': '1000',
                                                                  '@accumulation': '0',
                                                                  '@binning': '1',
                                                                  '@brightness': '0',
                                                                  '@digitalGain': '0',
                                                                  '@exposure': '708',
                                                                  '@gain': '3',
                                                                  '@lines': '1',
                                                                  'imageOffsetX': '24',
                                                                  'imageOffsetY': '24',
                                                                  'imageSizeX': '2000',
                                                                  'imageSizeY': '2000',
                                                                  'transform': '1'},
                                            'IntensifierField': '0',
                                            'Mode': 'CT3D',
                                            'PanelScan': 'false',
                                            'PanelScanNumberImages': '1',
                                            'StandardCorrection': 'false',
                                            'TiltDegrees': '0',
                                            'UsesMultipleXrayFilters': 'false',
                                            'WhiteTargetLevel': '58500'},
               'TallSampleRadius': '0',
               'TubeWarmUpTimeSeconds': '0',
               'UseTallSampleROI': 'false',
               'VGInLineWatchFolder': None,
               'VolumeGraphicsMacros': None,
               'VolumeGraphicsMacrosSupportFiles': None,
               'VolumeGraphicsVersion': '0',
               'VolumeOfInterest': {'XEnd': '999',
                                    'XStart': '0',
                                    'YEnd': '999',
                                    'YStart': '0',
                                    'ZEnd': '999',
                                    'ZStart': '0'},
               'XrayHead': 'Transmission',
               'XrayHeadNumber': '2',
               'XraySettings': {'FocusMode': 'autoDefocus',
                                'kV': '90',
                                'uA': '32'},
               'preprocessingType': '-1',
               'requiresPreprocessing': 'false'}}

:download:`sample_name.ctprofile.xml <../demo/nikon/Lego_alignment test_1 [2023-10-18 11.22.08]/Lego_alignment test_1.ctprofile.xml>`

Rigaku

Rigaku instruments generate the meta-data files stored in two folders:

  1. CT_sample_name containg data collection paramenters
  2. CR_sample_name containg data analysis paramenters

List of files stored in the CT_sample_name folder:

  1. :download:`AutoCU_values.csv <../demo/rigaku/CT_20230720_093515/AutoCU_values.csv>`
  2. :download:`CT_20230720_093515.VIF <../demo/rigaku/CT_20230720_093515/CT_20230720_093515.VIF>`
  3. :download:`CT_20230720_093515.xml <../demo/rigaku/CT_20230720_093515/CT_20230720_093515.xml>`
  4. :download:`CT_20230720_093515_th.jpg <../demo/rigaku/CT_20230720_093515/CT_20230720_093515_th.jpg>`
  5. :download:`DataInfo.xml <../demo/rigaku/CT_20230720_093515/DataInfo.xml>`

List of files stored in the CR_sample_name folder:

  1. :download:`1K_Recon_15_Long_High Resolution.prm <../demo/rigaku/CR_20230720_093515/1K_Recon_15_Long_High Resolution.prm>`
  2. :download:`512_Recon_15_Long_High Resolution.prm <../demo/rigaku/CR_20230720_093515/512_Recon_15_Long_High Resolution.prm>`
  3. :download:`Angle.prm <../demo/rigaku/CR_20230720_093515/Angle.prm>`
  4. :download:`BHCData.csv <../demo/rigaku/CR_20230720_093515/BHCData.csv>`
  5. :download:`CR_20230720_093515.RIF <../demo/rigaku/CR_20230720_093515/CR_20230720_093515.RIF>`
  6. :download:`CR_20230720_093515_th.jpg <../demo/rigaku/CR_20230720_093515/CR_20230720_093515_th.jpg>`
  7. :download:`Full_Recon_15_Long_High Resolution.prm <../demo/rigaku/CR_20230720_093515/Full_Recon_15_Long_High Resolution.prm>`
  8. :download:`Recon.mnri <../demo/rigaku/CR_20230720_093515/Recon.mnri>`
  9. :download:`Recon.prm <../demo/rigaku/CR_20230720_093515/Recon.prm>`

Scanco

Scanco instruments save data and the meta-data an ISQ file.

The meta-data are saved in the header of the ISQ file. ISQ Header format of an ISQ files consist of a standard 512-byte header, optional extended header blocks and the data part. Because the size of the extended header can vary, one has to read the data-offset (last 4 bytes of the 512-byte header) to be able to get to the start of the data (image) part. The offset is in 512-byte blocks, meaning if you encounter a value of 6, the data starts at byte 3584 (512 for standard header + 6x512 for the extended header).

Here is the header structure in c code:

typedef struct {
/*---------------------------------------------*/
char check[16];
int data_type;
int nr_of_bytes; /* either one of them */
int nr_of_blocks; /* or both, but min. of 1 */
int patient_index; /* 1 block = 512 bytes */
int scanner_id;
int creation_date[2];
/*---------------------------------------------*/
int dimx_p;
int dimy_p;
int dimz_p;
int dimx_um;
int dimy_um;
int dimz_um;
int slice_thickness_um; /* not used anymore */
int slice_increment_um; /* not used anymore */
int slice_1_pos_um;
int min_data_value;
int max_data_value;
int mu_scaling; /* p(x,y,z)/mu_scaling = value [1/cm] */
int nr_of_samples;
int nr_of_projections;
int scandist_um;
int scanner_type;
int sampletime_us;
int index_measurement;
int site; /* Coded value */
int reference_line_um;
int recon_alg; /* Coded value */
char name[40];
int energy; /*V */
int intensity; /* uA */
int fill[83];
/*---------------------------------------------*/
int data_offset; /* in 512-byte-blocks */
} ima_data_type, *ima_data_typeP;

The first 16 bytes are a string 'CTDATA-HEADER_V1', used to identify the type of data.

The 'int' are all 4-byte integers.

dimx_p is the dimension in pixels, dimx_um the dimension in microns.

So dimx_p is at byte-offset 44, then dimy_p at 48, dimz_p (=number of slices) at 52.

The microCT calculates so called 'x-ray linear attenuation' values. These (float) values are scaled with 'mu_scaling' (see header, e.g. 4096) to get to the signed 2-byte integers values that we save in the .isq file. e.g. Pixel value 8192 corresponds to lin. att. coeff. of 2.0 [1/cm] (8192/4096)

Following to the headers is the data part. It is in 2-byte short integers (signed) and starts from the top-left pixel of slice 1 to the left, then the next line follows, until the last pixel of the last sclice in the lower right.

meta-data

You can extract the Scanco meta-data using the provided python reader (see Meta-data readers section on this website).

"CalibrationData": "",
"CreationDate": "16-AUG-2023 14:32:47.206",
"DataRange": [
    -21716.0,
    32767.0
],
"Energy": 55.0,
"Intensity": 0.145,
"MeasurementIndex": 24292,
"ModificationDate": "16-AUG-2023 14:32:47.206",
"MuScaling": 4096.0,
"MuWater": 0.7032999992370605,
"NumberOfProjections": 1000,
"NumberOfSamples": 2000,
"PatientIndex": 9130,
"PatientName": "SB_WT_G3955",
"ReconstructionAlg": 3,
"ReferenceLine": 37.704,
"RescaleIntercept": -1000.0,
"RescaleSlope": 0.34713582434927287,
"RescaleType": 0,
"RescaleUnits": "",
"SampleTime": 200.0,
"ScanDistance": 12.0,
"ScannerID": 4274,
"ScannerType": 10,
"Site": 4,
"SliceIncrement": 0.006,
"SliceThickness": 0.006,
"Version": "CTDATA-HEADER_V1",
"direction": [
    [
        1.0,
        0.0,
        0.0
    ],
    [
        0.0,
        1.0,
        0.0
    ],
    [
        0.0,
        0.0,
        1.0
    ]
],
"origin": [
    0.0,
    0.0,
    0.0
],
"spacing": [
    0.006,
    0.006,
    0.006
]}

Sigray

Sigray instrument generates HDF files. A meta-data reader is available at hdf reder

meta-data

Meta data name Value Units dimension
/measurement/instrument/detector/binning_x 1   (2401,)
/measurement/instrument/detector/binning_y 1   (2401,)
/measurement/instrument/detector/dimension_x 2048 pixel (2401,)
/measurement/instrument/detector/dimension_y 2048 pixel (2401,)
/measurement/instrument/detector/exposure_time 15 s (2401,)
/measurement/instrument/detector/manufacturer Andor   (2401,)
/measurement/instrument/detector/name detector   (1,)
/measurement/instrument/detector/objective_magnification 1   (1,)
/measurement/instrument/detector/operating_temperature -59.88 C (2401,)
/measurement/instrument/detector/physical_pixel_size 0.099 um (1,)
/measurement/instrument/detector/pixel_size_x 0.65 um ()
/measurement/instrument/detector/pixel_size_y 0.65 um ()
/measurement/instrument/detector/setup/andor_y 1.2 um (2401,)
/measurement/instrument/detector/setup/andor_z -0.2039 um (2401,)
/measurement/instrument/detector/setup/detector_x -714.91 um (2401,)
/measurement/instrument/detector/setup/detector_z 377000.0 um (2401,)
/measurement/instrument/detector/setup/focus_x -9673621.25 um (2401,)
/measurement/instrument/detector/setup/focus_y 0 um (2401,)
/measurement/instrument/detector/setup/shadobox_y 0 um (2401,)
/measurement/instrument/detector/translation/geometry/andor_y_offset 3713309.12 um (2401,)
/measurement/instrument/detector/translation/geometry/andor_z_offset 221051.84 um (2401,)
/measurement/instrument/detector/translation/geometry/detector_x_offset 1449070.128 um (2401,)
/measurement/instrument/detector/translation/geometry/detector_z_offset -2930182.356 um (2401,)
/measurement/instrument/detector/translation/geometry/focus_x_offset 1296.875 um (2401,)
/measurement/instrument/detector/translation/geometry/focus_y_offset 0 um (2401,)
/measurement/instrument/detector/translation/geometry/shadobox_y_offset 3777088.28 um (2401,)
/measurement/instrument/grid/name grid   (1,)
/measurement/instrument/grid/setup/grid1_pitch -400 um (2401,)
/measurement/instrument/grid/setup/grid1_roll -4000 um (2401,)
/measurement/instrument/grid/setup/grid1_x -3971.8319999999367 um (2401,)
/measurement/instrument/grid/setup/grid1_y -1440.0 um (2401,)
/measurement/instrument/grid/setup/grid1_yaw 0 um (2401,)
/measurement/instrument/grid/setup/grid1_z 2633983.904 um (2401,)
/measurement/instrument/grid/setup/grid2_pitch 0 um (2401,)
/measurement/instrument/grid/setup/grid2_roll 0 um (2401,)
/measurement/instrument/grid/setup/grid2_x -3748028.856 um (2401,)
/measurement/instrument/grid/setup/grid2_y -9600480.625 um (2401,)
/measurement/instrument/grid/setup/grid2_yaw 0 um (2401,)
/measurement/instrument/grid/setup/grid2_z 3787210.864 um (2401,)
/measurement/instrument/grid/translation/geometry/grid1_pitch_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid1_roll_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid1_x_offset 3751429.484 um (2401,)
/measurement/instrument/grid/translation/geometry/grid1_y_offset 42354.53125 um (2401,)
/measurement/instrument/grid/translation/geometry/grid1_yaw_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid1_z_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid2_pitch_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid2_roll_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid2_x_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid2_y_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid2_yaw_offset 0 um (2401,)
/measurement/instrument/grid/translation/geometry/grid2_z_offset 0 um (2401,)
/measurement/instrument/sample/name sample   (1,)
/measurement/instrument/sample/setup/sample_x 64807.5 um (2401,)
/measurement/instrument/sample/setup/sample_y 25105.663999999873 um (2401,)
/measurement/instrument/sample/setup/sample_z 63552.5 um (2401,)
/measurement/instrument/sample/translation/geometry/sample_theta_offset 0 um (2401,)
/measurement/instrument/sample/translation/geometry/sample_x_offset 0 um (2401,)
/measurement/instrument/sample/translation/geometry/sample_y_offset -3729685.164 um (2401,)
/measurement/instrument/sample/translation/geometry/sample_z_offset 0 um (2401,)
/measurement/instrument/source/name source   (1,)
/measurement/instrument/source/setup/source_x -710.0400000000373 um (2401,)
/measurement/instrument/source/setup/source_z -63000.0 um (2401,)
/measurement/instrument/source/translation/geometry/source_x_offset 3711240.0 um (2401,)
/measurement/instrument/source/translation/geometry/source_z_offset -2245421.668 um (2401,)
/process/acquisition/image_exposure_time 15 s (2401,)
/process/acquisition/image_is_complete 1   (2401,)
/process/acquisition/setup/angular_step 0.15 deg (2401,)
/process/acquisition/setup/number_of_projections 2401   (2401,)
/process/acquisition/setup/rotation_end_angle 180 deg (2401,)
/process/acquisition/setup/rotation_start_angle -180 deg (2401,)
/process/name absorption_tomography   (1,)

layout

│
├── exchange
│   │
│   ├── data (1901, 1152, 1470)
│   ├── data_dark (1152, 1470)
│   ├── data_white (1152, 1470)
│   └── theta (1901,)
├── implements ()
├── measurement
│   └── instrument
│       │
│       ├── detector
│       │   │
│       │   ├── binning_x (2401,)
│       │   ├── binning_y (2401,)
│       │   ├── dimension_x (2401,)
│       │   ├── dimension_y (2401,)
│       │   ├── exposure_time (2401,)
│       │   ├── manufacturer (2401,)
│       │   ├── name (1,)
│       │   ├── objective_magnification (1,)
│       │   ├── operating_temperature (2401,)
│       │   ├── output_data (1,)
│       │   ├── physical_pixel_size (1,)
│       │   ├── pixel_size_x ()
│       │   ├── pixel_size_y ()
│       │   ├── setup
│       │   │   │
│       │   │   ├── andor_y (2401,)
│       │   │   ├── andor_z (2401,)
│       │   │   ├── detector_x (2401,)
│       │   │   ├── detector_z (2401,)
│       │   │   ├── focus_x (2401,)
│       │   │   ├── focus_y (2401,)
│       │   │   └── shadobox_y (2401,)
│       │   └── translation
│       │       └── geometry
│       │           │
│       │           ├── andor_y_offset (2401,)
│       │           ├── andor_z_offset (2401,)
│       │           ├── detector_x_offset (2401,)
│       │           ├── detector_z_offset (2401,)
│       │           ├── focus_x_offset (2401,)
│       │           ├── focus_y_offset (2401,)
│       │           └── shadobox_y_offset (2401,)
│       ├── grid
│       │   │
│       │   ├── name (1,)
│       │   ├── setup
│       │   │   │
│       │   │   ├── grid1_pitch (2401,)
│       │   │   ├── grid1_roll (2401,)
│       │   │   ├── grid1_x (2401,)
│       │   │   ├── grid1_y (2401,)
│       │   │   ├── grid1_yaw (2401,)
│       │   │   ├── grid1_z (2401,)
│       │   │   ├── grid2_pitch (2401,)
│       │   │   ├── grid2_roll (2401,)
│       │   │   ├── grid2_x (2401,)
│       │   │   ├── grid2_y (2401,)
│       │   │   ├── grid2_yaw (2401,)
│       │   │   └── grid2_z (2401,)
│       │   └── translation
│       │       └── geometry
│       │           │
│       │           ├── grid1_pitch_offset (2401,)
│       │           ├── grid1_roll_offset (2401,)
│       │           ├── grid1_x_offset (2401,)
│       │           ├── grid1_y_offset (2401,)
│       │           ├── grid1_yaw_offset (2401,)
│       │           ├── grid1_z_offset (2401,)
│       │           ├── grid2_pitch_offset (2401,)
│       │           ├── grid2_roll_offset (2401,)
│       │           ├── grid2_x_offset (2401,)
│       │           ├── grid2_y_offset (2401,)
│       │           ├── grid2_yaw_offset (2401,)
│       │           └── grid2_z_offset (2401,)
│       ├── sample
│       │   │
│       │   ├── name (1,)
│       │   ├── setup
│       │   │   │
│       │   │   ├── sample_theta (2401,)
│       │   │   ├── sample_x (2401,)
│       │   │   ├── sample_y (2401,)
│       │   │   └── sample_z (2401,)
│       │   └── translation
│       │       └── geometry
│       │           │
│       │           ├── sample_theta_offset (2401,)
│       │           ├── sample_x_offset (2401,)
│       │           ├── sample_y_offset (2401,)
│       │           └── sample_z_offset (2401,)
│       └── source
│           │
│           ├── name (1,)
│           ├── setup
│           │   │
│           │   ├── source_x (2401,)
│           │   └── source_z (2401,)
│           └── translation
│               └── geometry
│                   │
│                   ├── source_x_offset (2401,)
│                   └── source_z_offset (2401,)
└── process
    │
    ├── acquisition
    │   │
    │   ├── image_exposure_time (2401,)
    │   ├── image_is_complete (2401,)
    │   ├── image_theta (2401,)
    │   └── setup
    │       │
    │       ├── angular_step (2401,)
    │       ├── number_of_projections (2401,)
    │       ├── rotation_end_angle (2401,)
    │       └── rotation_start_angle (2401,)
    └── name (1,)

Tescan

Tescan instrument generates the following meta-data file:

in the raw data directory:

  1. :download:`script_executed.txt <../demo/tescan/script_executed.txt>`
  2. :download:`script.txt <../demo/tescan/script.txt>`
  3. :download:`scan settings.txt <../demo/tescan/scan settings.txt>`
  4. :download:`data settings XRE.txt <../demo/tescan/data settings XRE.txt>`
  5. :download:`data set settings.ini <../demo/tescan/data set settings.ini>`
  6. :download:`Acquisition settings XRE.txt <../demo/tescan/Acquisition settings XRE.txt>`

recon folder:

  1. :download:`reconreport.html <../demo/tescan/recon/reconreport.html>`
  2. :download:`geometry recon.txt <../demo/tescan/recon/geometry recon.txt>`
  3. :download:`data settings xre recon.txt <../demo/tescan/recon/data settings xre recon.txt>`

UCL

Univesity College London Edge Illumination instrument generates the following meta-data file:

  1. :download:`scan_parameters.txt <../demo/ucl/scan_parameters.txt>`

meta-data

[System]

Owner UCL Maximum
Scanner Edge Illumination 007Mo
Location 2.09a
Source Rigaku 007
Target Molybdenum
Detector Hamamatsu C9732DK
Camera Pixel Size [um] 50
Source to detector distance [m] 0.86
Source to sample mask distance [m] 0.68
Source to sample [m] 0.70
Detector to detector mask distance [m] 0.01
Sample mask pitch [um] 79
Sample mask aperture [um] 10
Detector mask pitch [um] 98
Detector mask aperture [um] 17
Masks type Skipped

[Parameters of the CT SCAN]

Saving_path C:/Users/test
IC_centre -28.000
IC_span 0.077
IC_No_points 11
IC_positions_scan -0.001,0,0.001,0.2
Exposure_time 1.2
Motor_No_Sample_Mask 1
G 1.0204
No_dithering 1
sample_IN_position 25.0
sample_OUT_position -50.0
Motor_No_Sample_X 6
Motor_No_Sample_ROTY 7
No_projections 1000
angular_range 360
how_many_projection_before_flat 200
how_many_images_per_flat_step 5
how_many_images_per_scan_step 1
start_from_projection 0
sub_acquisition_start 0
jitter_flag 1
extra_projection_flag 1

Zeiss

Zeiss Xradia instrument use a proprietary xrm/txrm data and meta data format. A python reader is avaialble at DXChange .

../img/meta_zeiss.png

meta-data

facility None
image_width 1024
image_height 1024
data_type 5
number_of_images 1601
pixel_size 9.405327796936035
reference_filename  
reference_data_type 10
thetas