Frequently Asked Questions « Neutron Imaging

Before your beam time
How do I submit a proposal?
- To learn more about submitting a proposal for beam time, go to neutrons.ornl.gov/users.
- To submit your proposal, go to the proposal system.
Where can I stay?

A few options are available off-site and on-site. Check the neutron.ornl.gov users page for more information.

How to request access to the analysis computers

Request access by going to https://xcams.ornl.gov/

During your beam time

I forgot my XCAMS password

Simply go to How to reset password web page.

How can I browse my data?

Use ONCat (tutorial here).

view your data
view the metadata and get infos about such or such data set
find an experiment using keyword
More features coming soon

How can I get help analyzing my data?

Contact Jean Bilheux to discuss your needs.

By going over your experiment together, Jean will show you how to run the current tools and will develop customed python notebooks if needed.

What are those “Jupyter notebooks”?

The Jupyter notebooks developed by Jupyter are an easy way to run python code using only a browser. By accessing our analysis computer, you won’t have anything to install. Refer to our How To page to learn how to do that.

Where are my data and how can I access them?

The following tutorial will show you where are your data and how you can access them. Just go to How To > Access your data.

I get a firefox error message when trying to start the Jupyter notebooks on the analysis machine.

After double clicking the [start jupyter] icon, I get a Firefox error message telling me that I have another Firefox window opened.

To fix this issue, just open a terminal and type >rm -rf ~/.mozilla

This should fix your issue and you should be able to start the Jupyter notebooks now.

Where do I find ImageJ (FiJi) on the analysis computer?

Just follow the following path to find and start ImageJ.

If you need to learn how to use ImageJ, check there tutorial web site.

What are the “metadata” and what do they mean?

You can retrieve the metadata of your TIFF images using:

ONCat
the Jupyter notebook list_tiff_metadata.ipynb

Tag Name	Description
ImageWidth	The number of columns in the image
ImageHeight	The number of rows in the image
BitsPerSample	The number of bits per component (ie. 16-bits or 32-bits for each greyscale pixel in our case)
SampleFormat	Specifies how to interpret each data sample in a pixel (1 = unsigned integer)
SamplesPerPixel	The number of components per pixel (1 in our case, which is grey scale)
Compression	1 = None
PhotometricInterpretation	1 = Min is black
MakeStr	The detector manufacture (eg. ‘Andor’ or ‘SBIG’)
ModelStr	The detector model number
SoftwareStr	EPICS areaDetector

Tags 65000 to 650009 have no name and are used for timestamps and a unique ID

Tag Name	Description
65000	EPICS timestamp. The timestamp is made when the image is read out from the camera. Format is seconds.nanoseconds since Jan 1st 00:00 1990.
65001	Unique ID for the image. Always 1 for single image acquisition, and incrementing up for camera and CT scans. Should always match the ImageCounter value.
65002	EPICS timestamp (seconds part only)
65003	EPICS timestamp (nanoseconds part only)

Scan Information

Tag Name	Description
FileNameStr	The original file name part of the constructed file name (see below)
InstrumentStr	‘CG1D’ or ‘VENUS’
IPTS	IPTS Number
ITEMS	ITEMS Number
SampleDescStr	Sample description (user entered)
NotesStr	User notes
DataSetStr	‘2D’ or ‘3D’
DataAcqModeStr	‘White Beam’, ‘TOF-cold/thermal’, ‘Epithermal’ or ‘Monochromatic’
DataTypeStr	‘OB’, ‘Raw’ or ‘DF’

Camera/Image Information

Tag Name	Description
ExposureTime	Exposure time for the image (in seconds)
ExposurePeriod	Exposure period for the image (Exposure Time + Readout Time in seconds). Not relevant for single image exposures.
NumImages	1= single image exposure (our normal mode of operation)
ImageCounter	Always 1 for single image acquisition, and incrementing up for camera and CT scans.
MinX	Min X pixel (0 for full frame images)
MinY	Min Y pixel (0 for full frame images)
SizeX	Size of image in X dimension (should be equal to the ImageWidth value)
SizeY	Size of image in Y dimension (should be equal to the ImageLength value)
Temperature	The setpoint temperature (in C)
TemperatureActual	The actual temperature read from the detector (in C)

Motor Position & Scan Device

Tag Name	Description
MotScanDeviceStr	‘Small Rot’ or ‘Large Rot’ used for this CT scan (if we are doing a camera scan or single image acquisition, this is not relevant)
RotationActual	Actual position of the rotation stage used in the CT scan (or the previous scan if we are doing a camera scan or single image acquisition)
MotRotTable.RBV	Large rotation table actual position
MotRotTable	Large rotation table setpoint
MotSmallRotTable.RBV	Small rotation table actual position
MotSmallRotTable	Small rotation table setpoint
MotLiftTable.RBV	Lift Table actual position
MotLiftTable	Lift table setpoint
MotShortAxis.RBV	Short axis actual position
…

TIFF file header example

TIFF Directory at offset 0x800008 (8388616)
  Image Width: 2048 Image Length: 2048
  Bits/Sample: 16
  Sample Format: unsigned integer
  Compression Scheme: None
  Photometric Interpretation: min-is-black
  Samples/Pixel: 1
  Rows/Strip: 2048
  Planar Configuration: single image plane
  Make: Unknown
  Model: Unknown
  Software: EPICS areaDetector
  Tag 65000: 837380408.136687
  Tag 65001: 1
  Tag 65002: 837380408
  Tag 65003: 148080423
  Tag 65010: FileNameStr:TiffHeaderTests
  Tag 65011: InstrumentStr:CG1D
  Tag 65012: IPTS:17255
  Tag 65013: ITEMS:-1
  Tag 65014: SampleDescStr:polarization test
  Tag 65015: NotesStr:polarization test
  Tag 65016: DataSetStr:2D
  Tag 65017: DataAcqModeStr:White Beam
  Tag 65018: DataTypeStr:Raw
  Tag 65019: ModelStr:DW936_BV
  Tag 65020: ManufacturerStr:Andor
  Tag 65021: ExposureTime:1.000000
  Tag 65022: ExposurePeriod:5.451660
  Tag 65023: NumExposures:1
  Tag 65024: NumImages:1
  Tag 65025: ImageCounter:1
  Tag 65026: MinX:0
  Tag 65027: MinY:0
  Tag 65028: SizeX:2048
  Tag 65029: SizeY:2048
  Tag 65030: Temperature:-60.000000
  Tag 65031: TemperatureActual:-57.830002
  Tag 65032: MotScanDeviceStr:Small Rot
  Tag 65033: RotationActual:183.000132
  Tag 65034: MotLiftTable.RBV:247.500452
  Tag 65035: MotLiftTable:247.500452
  Tag 65036: MotShortAxis.RBV:76.000000
  Tag 65037: MotShortAxis:76.000000
  Tag 65038: MotLongAxis.RBV:193.016000
  Tag 65039: MotLongAxis:193.016000
  Tag 65040: MotRotTable.RBV:182.996500
  Tag 65041: MotRotTable:183.000000
  Tag 65042: MotSmallRotTable.RBV:183.000132
  Tag 65043: MotSmallRotTable:183.000000
  Tag 65044: MotDetTable.RBV:200.000000
  Tag 65045: MotDetTable:200.000000
  Tag 65046: MotCameraVert.RBV:-51.699796
  Tag 65047: MotCameraVert:-51.699796
  Tag 65048: MotHoriTrans.RBV:28.000000
  Tag 65049: MotHoriTrans:28.000000
  Tag 65050: MotVertTrans.RBV:60.000000
  Tag 65051: MotVertTrans:60.000000
  Tag 65052: MotDiffuser.RBV:86.300000
  Tag 65053: MotDiffuser:86.300000
  Tag 65054: MotAperture.RBV:138.700000
  Tag 65055: MotAperture:138.700000
  Tag 65056: MotSlitVB.RBV:39.969938
  Tag 65057: MotSlitVB:39.969938
  Tag 65058: MotSlitVT.RBV:39.860484
  Tag 65059: MotSlitVT:39.860484
  Tag 65060: MotSlitHR.RBV:40.000000
  Tag 65061: MotSlitHR:40.000000
  Tag 65062: MotSlitHL.RBV:39.977781
  Tag 65063: MotSlitHL:39.977781
  Tag 65064: AndorCCDCooler:1
  Tag 65065: AndorCCDTempStatusStr:Not stabilized at set point
  Tag 65066: AndorCCDPreAmpGain:0
  Tag 65067: AndorCCDADCSpeed:2