DINGO USER MANUAL
Contents
1. DINGO User manual This guide is not intended to replace your local contact but to jog your memory if you are operating independently Anything strange call your local contact Numbers for DINGO instrument scientists Ulf Garbe office 7217 Floriana Salvemini office 7591 Klaus Dieter Liss office 9479 Joseph Bevitt office 7232 DINGO status 15 visible from outside Ansto at the following webpage http www nbi ansto gov au dingo Reactor status and cold source temperature visible at do not leave this webpage open for long periods of time http prism nbi ansto gov au reactor ReactorInfo swf Other useful numbers Emergencies 888 not emergency working alone form etc 3434 Health Physics 9779 IT helpdesk 9200 Feedback on the manual filomens ansto gov au Table of content 4 4 GENERAL 4 5 OPENING AND CLOSING THE SAMPLE BEAM SHUTTER 4 6 STARTING AN EXPERIMENT 4 7 DETECTOR CONFIGURATION 4 8 LUNCHING AN EXPERIMENT 5 QUICK GUIDE TO DATA RECONSTRUCTION 6 QUICK GUIDE TO DATA VISUALIZATION AND EVALUATION 7 BEFORE YOU LEAVE 1 RESPONSIBILITIES 1 1 The Head Bragg Institute has overall responsibility for the implementation of this work instruction within the Bragg Institute 1 2 The Head Bragg Institute is responsible for Nominating the OPAL NBI Source Officer Nominating Instrument Scientists for each NBI at the OPAL NBF 1 3 The OPAL NBI Source Officer has the following re2. a select directory 13 i use decomposed data folder decomp Select open beam images first open beam image Select dark images first dark image IF ob amp di images are stacked images i e not 5x separate files but 5 images within one file then i Open ImageJ ii Do the following for both di and ob stacked images 1 Open image sequence Despeckle Remove outliers Then save as image sequence Label di SampleX or ob SampleX PU EM dee OMA Save to decomp folder 3 Data parameters a b C d For Last angle specify 360 or 180 or other applicable value Assign pixel size in mm Tilt leave at O OK 4 Preparation crop images m uw Select directory decomp folder Select directory for resized images accept default called resized OK Trim image from left to right Accept 5 Preparation filter spots a b C Select directory of images resized folder Select directory for cleaned images default folder clean To remove random spots i Need to modify the custom level 1 Will need to experiment with various values 2 Aim for a fraction filtered value 0 01 0 01596 for Gadox scintillator 3 Aim for a fraction filtered value 0 196 for Lithium Fluoride scintillator 6 Preparation Normalise images Select folder for clean Do you want to normalise for beam intensity YES Select an area which does not incl
3. clicking on the Focus button the dataset will also be centered i e jump to the slice in the middle of the dataset 17 All interaction with the data in the 3D window takes place directly in the window itself The shortcut icons to change between the different modes of interaction with the 3D data is shown below 4 Rotate mode y Move mode If the Rotate mode 15 selected the current object is rotated by dragging the mouse pointer in the 3D window while holding the left mouse button pressed Pressing and holding the middle mouse button will spin the object around the axis through the window In Move mode pressing and holding the left mouse button will drag the object across the screen Pressing and holding the middle mouse button will zoom in or out A quick double click with the middle mouse button in the 3D window switches between the Rotate and Move mode Pressing the Center and focus camera button will re center and refit the 3D window on the currently selected object Hereafter you can find a step by step guide for basic actions 1 File import image stack i Directory D reconstructed ii Next iii Insert pixel sizes in resolution fields all X Y Z axes should be the same for all values IV Preview 1 Trim dataset to minimise size a Dothis via Top Right and Front projections V Next vi Finish 2 Additional filtering l Median filter or Gaussian filter may help 3 Registration l For changing th
4. you in how to enter the enclosure and load samples Before you do this independently you must sign the training form to acknowledge you have received the training The sample shutter may only be opened after going through the interlock procedure and ensuring no one is in the instrument area This procedure 1s 4 2 1 The NBI Operator activates the interlock by pressing the lockup initiation exit button located in the instrument area with the exit door closed 4 2 2 Visible and audible warnings will indicate the sequence has been initiated 4 2 3 All present in the instrument area must move into the instrument cabin and within 20 seconds the door must be closed This is locked by the SIS Only then will it be possible to open the beam E stops in the instrument area or control cabin can be used but they also close the secondary shutters An abort button may be used to stop the procedure This is located next to the exit button in the instrument area 4 2 4 The beam is then opened using the safety control panel The operation of the interlock system is specified in NBIP ER 4 3 STARTING AN EXPERIMENT 4 3 1 DINGO has a number of operating parameters which are determined before running an experiment usually by the instrument scientist These are controlled using the instrument control server SICS The main control parameters are the camera box position dz the camera translation stage position dy the motion of the sample st
5. age sx sy sz The SICS User Manual is provided in the instrument cabin SICS basic commands are listed below and they can be input by client Putty_ics1 please refer to pag 11 of the current manual for instructions on how to start client Putty_ics1 run motl posl mot2 pos2 success drive moti posi mot2 pos2 mot OR mot position mot hardposition mot list mot reset mot interest mot uninterest mot homerun 1 or 0 runs mot 1 to posi mot2to pos2 waits and blocks the command connection until all pending operations have finished or an interrupt occured 1s the same as run but it blocks the client that requested the drive from issuing commands until the motion has finished Can be called with one to n pairs of object new value pairs This command will set the variables in motion and wait until the driving has finished A drive can be seen as a sequence of a run command as stated above immediatly followed by a Success command prints the current position of the motor All zero point and sign corrections are applied prints the current position of the motor No corrections are applied Should read the same as the controller box Lists all the motor s parameters resets the motor parameters to default values This 1s software zero to 0 0 and software limits are reset to hardware limits initiates automatic printing of any position change of the motor This command 1s mainly interesting for implementors of sta
6. d cryomagnet 3 5 Before samples are removed from the OPAL NBF they must have an appropriate Clearance Certificate as described in PO P 004 3 6 For samples requiring special environmental conditions the Instrument Scientist must approve the experimental conditions obtain SAC approval and ensure that if relevant an Instruction Manual is provided 4 METHOD 4 GENERAL 4 1 1 All neutron scattering instruments must be used in accordance with Bragg Institute Procedure PO P 008 4 1 2 Samples are placed in holder or in air as appropriate to the instrument environment and experimental requirements 4 1 3 Details of the samples the instrument configuration and the environmental conditions may be recorded using the sample name sample description and sample title descriptors in the instrument data file in a manual log along with other relevant information such as details of personnel Proposal Number instrument configuration and Sample Environment used Note Generation of the electronic log is not automatic upon running a sample 4 1 4 Any operations to be performed by people within the Experimental Area must be performed while the sample shutter is closed It is forbidden for any person to be in the instrumental area while the shutter is open Access to the instrument area is mediated by the Safety Interlock System and described in section4 2 of this document 4 2 OPENING AND CLOSING THE SAMPLE BEAM SHUTTER Your local contact will train
7. e alignment of the sample ii Simple registration align the sample 4 Object Surface determination l Define both background and material with different 5 Rendering i Choose different renderers isosurface renderer volume renderer sum along ray li Opacity manipulation area 1 Slide red line across the until air is subtracted 2 Slide until fossils come into view rock will be removed too 18 3 Black line opacity curve can be used to define transparency 4 Right click on black line insert handle iii Optional disable or delete 1 Can be used to remove the air rock matrix delete permanent will remove useless data and speed things up iV A Appearance colour scale 1 Try using a preset selection e g rainbow spectrum 2 Setadditional handles on opacity manipulation area 3 Right click on appearance spectrum a Choose set colour between handles v Clipping plane box 1 Adds a plane box that can be made visible or invisible 2 Crops each plane individually 6 File save as l vgl file 7 Can save image screenshot Can save image stacks 9 Note Videos a Animation Keyframer mode classic i Centre animation 1 Unlock the object s Click the Navigation cursor button Hold Ctrl and left click where you want the centre of your animation In transformation window click on Centre on navigation cursor Load new animation setting e g a Default curves circle for circlin
8. e the rotating table moves Note a safety interlock is provided for sx sy and sz Refer to the instrument control software SICS manual to control change and check the parameters Once the sample position is optimized exit DINGO enclosure according to standard and safety procedure and then open the secondary shutter from the safety control panel Top view 100 100 Top view 270 lt 0 Neutron source sy Front view 70 CCD camera SZ Neutron source 300 4 4 LANCHING AN EXPERIMENT Ensure that DINGO Camera Server has been quit to avoid error message Start ANDOR from HP PC desktop DAV2 DINGO located in DINGO cabin Select the window Acquisition from the Command Menu P al Yii mids In order to take a radiographic image or to check the optimum exposure time in the sheet Setup camera select single Acquisition mode internal Triggering IMHz at 16 bit as Readout Rate Qn and input the Exposure time sec Click on the grey button in the Command Menu to start the acquisition If you want to save the shot select File Save as and then select directory where to store the file properly named with fits unsigned 16bit format Acquisition Setup image Orientation Video Mode Crop Readout Made Image Vertical Pixel Shift Exposure Time secs 60 0000 Shift Speed usecs 3855 Verlical Clock Voltage z Amplitude N
9. ertia Walt incor pos number of projections drive soma expr 0 d DUPLI clientput step angle number of accumulation per projection exposure time wait 20 to be inserted only if the acquisition of a second frame is needed to cover the whole volume of the sample drive drive high of the table stage drive soma 0 number of projections step angle number of accumulation per projection exposure time clientput uni number of dark current number of accumulation per dark current exposure time clientput tomography 12 When the script is ready press Esc on the keyboard then wq to save and quit the script Note the full list of commands for Vim text editor is availed at http www fprintf net vimCheatSheet html Y In order to start the scan go to ANDOR software Click on the grey button in the Command Menu and using client Putty type exe scan_soma_your tcl in the other open window S QUICK GUIDE TO DATA RECONSTRUCTION Copy your raw data from the folder previously defined in directory D to a new dedicate folder in network V from HP PC desktop DAV2 DINGO located in DINGO cabin Then you can operate the following procedure on the workstation available in DINGO cabin or on the dedicate windows machine locate in the Imaging room in H77 Open ImageJ software select File then Import from the Menu Command Select the directory with the raw data and click on the f
10. g through b Default curves clip for going through samples For further details about commands and procedure follow the instruction available on VGStudio MAX User Manual The Manual is available on DINGO cabin or can be consulted by selecting the Help button from the Command Menu 7 BEFORE YOU LEAVE Before you leave the instrument please Clean and return your sample holders Photocopy scan the relevant pages of the logbook Take all raw and treated data either using a thumb drive by burning the data to a CD DVD ask your local contact nicely or using ANSTO sharefile web based system at sharefile ansto gov au 19
11. he dedicate Ubuntu machine located in the Imaging room in H77 Start VGStudio MAX from the Windows Start menu You will see VGStudio MAX 2 2 with an empty scene f tt ss To launch the Import Wizard select File Import with the appropriate format of your input data Follow the instructions in the Import Wizard to specify how you would like your data imported The position of the slices is shown relative to the selected coordinate system The image below shows the locations of the function buttons in the 2D slice window hen 1 et ihr ER ON a Set brightness Toggle pan zoom mode Focus selected object With the Set brightness button selected the displayed Window Level similar to contrast and intensity of the slices can be changed Press and hold the left mouse button over the slice Dragging in an up down direction will change the Level and a left right direction changes the Window setting This feature is enabled by default and can be disabled in the Preferences The actual slice image can be moved by pressing and holding the middle mouse button To scroll through the slices use the mouse wheel Pressing and holding lt Ctrl gt combined with the mouse wheel will zoom in out With the pan zoom button selected the slice is moved using the left mouse button instead Pressing the Focus button will center and refit the slice window on the currently selected object By quickly double
12. i Try three or even four values iii Aim make line profile flat for both sample and background sections g Scan Adjust tilt i Right click tilt May need to choose different options i e adjust evaluation parameters until standard deviation shows flattening iii Then run with Evaluate iv Different slices may show differential tilt 1 represented by shadowing effects on reconstructed slices h Reconstruct volume i Choose slice near one end ii Iftilt is required for different parts of the specimens will need to reconstruct different sections of the sample separately 1 Forthis copy in same values from Quality section of Reconstruction txt notebook file that is saved in the Reconstruct folder into 2 Except tilt 3 Reconstruction iii After reconstruction 1 Rescale a Ensure that these values are consistent for all volumes 15 i This may require manually entering the values because the given spectrum may not include these b Rescaling will allow for smaller dataset and consistent contrasting i Donot delete temporary files 10 Optional Import reconstruction image sequence into ImageJ for orthogonal views a Click image stacks orthogonal views b Note Only possible once the scans have been reconstructed c Warning can make compy run quite slow 16 6 QUICK GUIDE TO DATA VISUALIZATION AND EVALUATION Operate on the workstation available in DINGO cabin or copy your reconstructed folder and use t
13. irst image Once the stack has been opened and visualized export the sequence of images as single files by selecting File Save as Image sequence and create a new folder where to save the decompressed data Repeat the procedure for all raw files Note the ful list of commands for lmageJ software 1 availed at http Amagej nih gow 1j docs index html When all data have been decompressed open Octopus software In the Menu Command select Other function and press Rename file Select Original path to import the decompressed files and rename them by writing the desired name in basename tag and distinguishing among beam profile dark current and projection images Octopus Reconstruction 8 8 Original path Shift numbersbasename Add zeros GF s 0 File names New File Names Current dataset info Processes executed Source directory D DakalPST Renamed datalclean Sh_ wb Projections SM wb 0000 gt SM wb 0625 Mr of beam profiles 0 Mr of offset images 0 gloverwrite Rename When the images stack is ready follow the instruction available on the Octopus Reconstruction User Manual The Manual is available on DINGO cabin or can be consulted by selecting the Help button from the Command Menu Please refer to the procedure described starting from section 6 Main window at pag 19 or to the following general guide 1 Open Octopus Octopus Reconstruction v 8 8 2 Select dataset
14. mperature to 90 C Input 0 5 s as exposure time Activate Multi on to set up a Server Dingo Camera Release 1 00 Jun 30 2014 Time Log Window Image Intensity Meta Data Histogram Surface 1 17 53 22 24 Camera Initialised Ready Camera Settings i Mhz Normal Gain 1x HS Bin 1x HistThreh 700 Exposr 0 50 s xStart 1 xEnd 2048 5 Temp 90 gt yStart 1 yEnd 2048 Single SOpen 150 SClose 200 ms Multi Off Config File Manage System Take Shot Clear Log HDFree 100 Gb Idle Temptr 31 C 16 Feb 2015 05 55 42 pm continuous camera acquisition and click on Take shot Manually focus the lens by twisting the focus ring by small steps You ll be able to see when the image is sharp by selecting the label Image from the top Command Menu in DINGO Camera Server You might have to twist the focus ring back and forth moving through and beyond your chosen point of focus until you see that focus is spot on and the grid is well visible Important notice When the image of the grid is sharp take note of the number of pixels that cover 10 mm by dragging the cursor on the two extreme lines of the grid that correspond to such distance Read the value on the tag that pops up on the captured image This information will be used to estimate the current pixel size and the field of view Replace the grid with the scintillator screen and cl
15. ormal t Honzontal Pixel Shift Gain High Sensinaty High Capacity Note Exposure Time Fire pulse length Baselne Baseline Clamp To set up a tomography scan in the sheet Setup camera select kinetic Acquisition mode external Triggering and MHz at 16 bit as Readout Rate Input the Exposure time the Number of Accumulations per each step angle and the Kinetic series length equal to the total number of images that will be acquired projections open beam dark current Note Parallel beam geometry requires projection images preferably with equiangular separation between 0 and 180 Ideal projections are images free of noise In practice this is never the case since noise is always present due to the statistical nature of the measurement Detectors need sufficient grey levels dynamic range If the detector 1s 12 bit or less one should acquire a number of images at every angle and use the sum or the average of these images The number of projections is theoretically defined as x x N 2 for 180 scans and zx x N for 360 scans where N is the number of row pixels that can see the transmitted image of the sample The number of projections can often be lower for practical applications but it is advisable to use a number of projections comparable or higher than the number of detector pixels in a single row More projections improve the statistics and quality of
16. ose the lid to check the focus for neutron Stick the Siemens star on the scintillator Exit DINGO enclosure according to standard safety procedure and then open the secondary shutter from remote control monitor 4 On DINGO Camera Server from PC desktop CCAM 1I DINGO input 5 s as exposure time 5 Activate Multi off and click on Take shot 6 When the neutron radiography is taken go to Meta Data in the top Command Menu and take note of the Sharpness factor 7 Using client Putty drive the camera translation table by incrementing and decrementing dy value by step of 0 5 8 Take a shot and check the Sharpness factor for each dy 9 Then set dy at the value showing the highest Sharpness factor Close the shutter from the safety control panel and enter DINGO enclosure according to standard and safety procedure Remove the Siemens star from the scintillator and place it back in its box 4 3 SAMPLE SET UP Place your sample properly allocated in the sample holder on the rotation stage Using client Putty drive the sample stage at sx to be centred with respect to the neutron beam and the detector Then adjust the high and the closest possible distance from the detector by setting sz and sy respectively see the common commands in section 4 3 1 of this document In the case of tomographic experiment be sure that the sample does not collide the scintillator or other component of the detector whil
17. sponsibilities and authorities to Ensure that the operation of the NBI complies with the OPAL NBF Source Licence Authorise nominated NBI Operators and Enable the opening of the secondary shutters 1 4 Instrument Scientists are to Ensure that persons comply with the latest applicable Bragg Institute Procedures and Instructions Nominate NBI Operators of their NBI according to PO P 011 Ensure this work instruction 1s implemented 1 5 Other responsibilities are detailed in section 5 of this work instruction 2 PREREQUISITES 2 1 A current SAC Approval form for DINGO must be displayed on the instrument 2 2 If Sample Environment Equipment is in use the relevant equipment instructions will be located in the instrument control cabin 3 PRECAUTIONS 3 1 An NBI Operator may only use DINGO with the approval of the Instrument Scientist except when NBF Staff are being trained in the operation of an NBI by an Instrument Scientist 3 2 When working with the DINGO instrument the operator must obey all radiation warning indicators and signs and follow all procedures required by the Safety Interlock System 3 3 Samples that are to be placed on the instrument must meet all necessary safety standards relating to toxicity flammability and radioactivity see PO P 004 3 4 Sample Environment equipment must only be used within specified tolerances see the specific work instructions for sample changer cryostats furnace pressure cells an
18. te TIFF data will not be post processed and vall therefore not be affected by data type hanstommations or onentation settings Data be split over multiple files Files other than the first will have 2 3 ete appended to the stem 10 Then click the button to save the configuration In order to create the external trig that will be read by the camera software start the Instrument Control Server SICS by running the client Putty_ics1 ae PuTTY pem lt gt Andor SOLIS me dingo sis E g ep dingolocal gp dingofastshutter gp Camera Server Calculator Tasks E Paint Run Pageant PulTYgen Andor SOLIS 32 bit Cygwin64 Terminal PuTTYgen X XLaunch System Information gt i 5 DingoServer exe Shortcut gt All Programs f Shutdown gt Log in using the account provided by your personal contact and type SICS client Then type cd batch to have access to the list of script available Open the reference script by writing vi scan_soma tcl and then input cp scan_soma tcl scan_soma_yourscan tcl to rename the script Finally vi scan_soma_yourscan tcl to open the script Press Insert or A on the keyboard in order to be able to modify the script Picture showing the essential value to modify 11 tertiar Open wait lt U number of open beam number of accumulation per open beam exposure time drive drive t
19. the size of the DINGO door enclosure or at the entrance of DINGO cabin Using client Putty drive the camera translation table dy to 125 If high intensity is needed the high of the camera box should be changed Using client Putty drive the camera translation table dz to 100 Ensure that the sample stage is at a proper distance to avoid any collision If not drive sx through client Putty Select the high intensity 20x20 tertiary shutter 4 from the safety control panel Note no safe interlock is provided for dy at the moment Be careful when driving dy since the lens can collide with the mirror mounted in front of the scintillator screen A safe value for dy is 45 Finally ensure that the camera lens diaphragm is fully open and the cap is taken off 4 2 1 CAMERA FOCUSING Once the detector has been configured the camera focus can be adjusted At the first stage the lens focus has to be optimized using light Partially close the lid of the camera box leaving a narrow slit to let the room light in Then replace the scintillator screen mounted on the nose with the millimetric grid sticked on the aluminium plate of the proper side The grid has to face towards the mirrors 1 Ensure that ANDOR software has been quit to avoid error message Start DINGO Camera Server from HP PC desktop CCAM 1 DINGO located on the left side when exit DINGO enclosure 3 Select the window Config from the Command Menu in the bottom and set the cooling te
20. the reconstruction but also increase the scanning times and reconstruction time Jon 3 zoa Timings Vertical Pixel Shift Exposure Time secs 60 0000 Shift Speed usecs 38 55 v Number of Accumulations een Voltage Minimum Trigger Period secs 64 5731 0 015886 Horizontal Pixel Shift Kinetic Series Length Pre Amplifier G ain ms Output amp mpllier 9 High Sensitivit Cosmic Ray Removal d High Capacity Note Exposure Time Fire pulse length Baseline Baseline Clamp Select sheet Binning and define the region of interest where your sample fit Then move to sheet Spooling end enable spooling Select Tif as file type and name the file and choose the directory D filer experiment data spool yourfolder Region of Interest Binning ex vor ng p F Update Display During Acquisition 10241024 O2xe Acquisition Sire MB 5240 e 512 4512 e 4x4 5lorame d Disk Available RAM MB 40 Available Disk Space 103116 t 256 256 8x8 Custom 16416 di em Dien vesperimenhvdatalspooy Lett 1 Right 2049 Formal unsigned 16 bit integer Open spooled data when complete Bottom Top 2048 1 jl 11 Use Append Settings Irom Autozave tab 4 Retain Absolute Coordinates m Dataset Drew gt gt E Perform binning in software No
21. tus display clients disables interest homerun with no arguments reports the current status a value of 1 means that the motors have been homed homerun 1 will run the homing routine Used on motors with relative encoders e g slit motors list mot type Returns the motor s type Warning Emergency stop in order to interrupt any motor driving type INT1712 3 4 2 DETECTOR CONFIGURATION According to the needed spatial resolution different reference configurations can be set up Pixel size of 25 um The standard set up is 100 mm lens mounted on the camera and the small nose with a field of view of 10x10 cm set in place Select the 5x5 tertiary shutter 1 from the safety control panel situated at the size of the DINGO door enclosure or at the entrance of DINGO cabin Using client Putty drive the camera translation table dy to 115 Picture Pixel size of 50 um The standard set up is 100 mm lens is mounted on the camera and the big nose with a field of view of 10x10 cm set in place Select the 10x10 tertiary shutter 2 from the safety control panel situated at the size of the DINGO door enclosure or at the entrance of DINGO cabin Using client Putty drive the camera translation table dy to 220 Pixel size of 100 um The standard set up is 50 mm lens is mounted on the camera and the big nose with a field of view of 20x20 cm set in place Select the 20x20 tertiary shutter 3 from the safety control panel situated at
22. ude the sample or sample container Select ring filter moderate e g 2 or 3 7 Preparation Correct axis tilt o p Note this process is a little shonky try it once or twice and if the tilt is too high it might not be working if so this can be corrected in reconstruction phase Select normalised folder Select folder select save and then current folder Select first image for projection at O degrees Select middle image for projection at 180 degrees 14 f Normalise projections with flat field NO g Selecta lateral slice area which includes the sample in all orientations i Ifthe tilt is consistent continue ii If not come back to later e g after parallel beam reconstruction 8 Preparation Sinograms a Selected rotated folder b Select sinograms folder new folder sinograms 9 Reconstruction parallel beam reconstruction a Select sinogram folder b Select reconstructed folder select default folder c Untick Exit on finish d Choose middle slice default slice i Scan Adjust rotation axis 1 right click rotation axis value ii Fixthe rotation for that slice this should balance the axis for whole sample iii Evaluate e Options Apply ring filter i Enter values of maximum ring width 1 Play around with it 2 too big data lost too small ring artifacts retained ii Reconstruct slice f Options Beam hardening correction i Two first values e g 0 05 0 05 x x i
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