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:
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:
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 |
[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:
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 |
[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 |
[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 |
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 |
[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 |
Rigaku¶
Rigaku instruments generate the meta-data files stored in two folders:
CT_sample_name containg data collection paramenters
CR_sample_name containg data analysis paramenters
List of files stored in the CT_sample_name folder:
List of files stored in the CR_sample_name folder:
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:
recon folder:
UCL¶
Univesity College London Edge Illumination instrument generates the following meta-data file:
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 .
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 |