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Vendor’s service manual is located in Desktop>Aeris>Aeris Diffractometer References.  Also on the orange Panalytical USB.  Backup PDF’s of the service manual are in IODP Share> IODP Technical Manual


The X-ray Laboratory onboard the R/V JOIDES Resolution preforms diffraction analyses of minerals, clays, and rock powders.

The laboratory uses a benchtop Malvern Panalytical AERIS Research Edition XRD. Associated software, HighScore Plus, allow for powder diffraction analysis of minerals, including peak matching, mineral, and chemical compound identification. The X-ray Laboratory provides the scientist with a quick and reliable tool for mineral identification; particularly useful for identifying fine-grained minerals or mixtures of alteration minerals. In addition, XRD data can be used to determine mineral proportion.

Theory of Operation

A mineral is a three-dimensional structure that forms a crystal lattice. When a focused X-ray beam is directed onto the crystal structure of a mineral, part of the beam is diffracted. X-rays are diffracted differently depending on the atomic composition and arrangement within the crystal lattice. Each mineral has a unique fingerprint that is determined based on a characteristic set of d-spacings (space between adjacent planes of atoms in the crystal lattice). This is a fundamental characteristic of minerals that allow mineral identification through X-ray diffraction. X-rays are generated in a vacuum tube and directed to a powdered sample, when the X-rays hit the powdered sample, they are diffracted onto a detector. The X-ray detector then converts the signal to a count rate. The angle between the X-ray tube, sample, and detector are varied during measurement to produce an X-ray scan . Using the angle between the X-ray tube, sample, and detector (2θ, which can be measured) and the wavelength of a generated X-ray beam (λ, which is known based on the material generating the X-rays), the scientist can determine the d-spacings by using Bragg's law:
nλ = 2dsinθ
n = order of the diffracted beam
λ = wavelength of the incident X-ray beam
d = distance between adjacent planes of atoms (d-spacings)
θ = angle of incidence of the X-ray beam
The d-spacings generated by an X-ray scan provide the unique fingerprint of the mineral or minerals present in the sample.

Instrument Apparatus and Hardware

  • Benchtop Malvern Panalytical AERIS Research Edition X-ray Diffractometer (XRD)
  • Goniometer
    • The goniometer is the core of the diffractometer. The goniometer radius is145 mm. The minim um step size for the angle of incidence (ro) and the scattering angle (28) is 0.001°.

  • X-ray Source, Copper (Cu)
    • The X-ray tube is made of ceramic. The anode is at a maximum of 40 kV above ground potential and is cooled with a glycol mixture of 25 % glycol and 75 % water.
    • The window of the X-ray tube is made of beryllium and is 300 µm thick.

  • PIXcel1D-Medipix3 dectector
    • Soller slits
    • Beta filter
    • Divergence slits
    • Beam mask
    • Beam knife
    • Si standard
    • Corundum standard
  • Sample Holders


When properly operated within the specifications, the radiation level at a distance of 10 cm from the outside surf ace of the instrument is less than 1 µSv/h.

The cover has a door lock to prevent accidents. As a safety measure, you cannot open the shutter of the X-ray tube if the cover is not correctly closed and locked. Other safety precautions are that you cannot open the cover when the shutter is open, when a goniometer arm moves, or when the instrument initializes.

You can open the lid while the xray warning lights are on.  The shutter of the tube remains closed which makes it safe to do so.  The instrument will not allow you to run a sample or open the shutter while the lid is open.

The closed circle icon on the screen indicates when the shutter is closed and it is safe to open the lid.

X-RAYS ON lamps on the top corners of the instrument and 2 more on the inside of the cover give a visual warning when high tension is applied to the X-ray tube.

The X-RAYS ON lamps are 'fail safe' lamps and they are part of the safety circuit.

The result is that if one of the lamps fails, no high tension can be applied to the instrument.

When you turn the HT keyswitch clockwise, the HT generator goes on. If the instrument is energized and the safety loops are closed, the HT generator is automatically set to 40 kV, 15 mA or 40 kV, 7.5 mA.

When the HT generator is in the ON condition, the indicators are as follows:

  • The kV and mA indicators on the touchscreen show the settings
  • The 4 X-RAYS ON lamps on the corners of the instrument are on.

When you turn the HT keyswitch counter-clockwise, the HT generator goes off .

The HT keyswitch is also used to reset the Xsafe system.

If the HT key is removed from the instrument and an  unsafe condition  is sensed, you  cannot switch the high  tension  on  again.

NOTE: The HT key can be removed and kept in a safe place.





  WARNING          Toxic MATERIAL  XRay tube windows and detector windows contain beryllium. 



Sample Preparation and Holders

Aeris sample holders cannot be interchanged with the Bruker sample holders. The size is slightly different and they are magnetic which lets the machine to know there is a sample in the slot.

Bulk Powder Backloading

Most common method is backloading. The sample holder is in two parts, the top ring and the base which the top ring clips into and is loaded using the sample table which is the small device with a center platform and three round buttons around it.
Follow the next steps along with the pictures on the next page to pack and assemble the backloaded sample holders.

1). Place the top ring upside down on the sample prep table and clip it in by pressing the button on the side. Take care not to scratch the center platform.
2). Mound the powder up slightly in a conical shape.
3.) With a blade or glass slide make chopping motions on the powder to help spread it out evenly.  Press it down with the cylindrical press.
4.) Scrape off the excess with a blade or glass slide.
5.) Brush away excess powder so that the outer ring is clean for attaching the sample holder base.
6.) Press and clip the sample holder base into the top ring. It should snap in cleanly and easily.
7.) Turn the entire sample prep table upside down, resting the sample holder base on the countertop, and press the release button on the side to release the completed sample holder. Sample surface should be flat and flush with the edge of the holder.  With the brush or kimwipe, clean any powder off the ring surface because that comes in contact with the sample spinner.


If the powder sticks to the sample table when you flip it upside down to release, try it again with a piece of weighing paper placed on top of the platform and then clip the top ring in.

If you don’t have enough power to fill the sample holder, after pressing down with the cylindrical press add one of the cardboard spacers so that the cardboard spacer is flush with the ring top and then clip in the holder base.

1.)1 2.)          3.)               4.)

5.)                                     6.)                                      7.) 

Add sample using spatula (A) and then place cardboard insert so that it is flush with the back of the sample holder (B), then attach the back of the holder. of there is too much sample the back will not attach.



Cleaning and disassembling sample holders

First check scan to make sure the counts etc are satisfactory. If the scan is acceptable poor sample back into sample bag. next remove top ring. the rig is magnetically connected and should pop off by hand (a). disassemble the rest of the sample holder. In the pictures below a cardboard spacer was used.  Rinse each piece with DI water and then isopropal alcohol with kim wipes.  Isopropal alcohol should remove the sharpy label on the front of the sample holder. Once clean and dry store back in box or use to make next sample.

a.                   b.

Small samples and slurry/smears

The following technique is modified from the U.S. Geological Survey Open-File Report 01-041, A Laboratory Manual for X-Ray Powder Diffraction. For a very small amount of sample material (i.e., end of a tooth pick), samples may be ground to a fine talc-like powder and smeared onto one of the silicone disk inserts. Although not useful for semiquantitative analysis, this method is useful for rapidly determining bulk mineralogy.

  1. Place a small amount of sample powder in the center of a silicone or single crystal quartz disk.
  2. Add 2–3 drops of 70 % isopropyl alcohol or distilled water to the sample. Note: Isopropyl dries faster than water.
  3. Spread the sample to a thin layer using a glass rod. The slurry should be spread evenly across the disk. If there is not enough material to cover the entire disk, concentrate the sample in the middle of the disk where the X-rays will contact the sample.
  4. Place the sample in the desiccator to dry before running in the XRD.

For extremely small amounts of sample or clay smear mounts use the sample rings, clip, aluminum spacer, and zero background silicon disks.  Do not scratch the mirrored silicon disks, always use an aluminum spacer so the clip does not scratch the surface.  A tiny amount of power can be mixed with alcohol to make a slurry and that is smeared in the center of the silicon disk.

Turn the ring upside down and place the silicon disk in the indentation.  Use the flat side or the side with the shallow well for your sample (different amount of sample flat vs well), depending on how much you have.  Put the aluminum spacer on the silicon disk, then press the clip in and turn it to secure both in place. 

If doing heating steps remove disc with sample and place on try to go in the oven. DO NOT heat the sample holders they will deform shape and will no longer be able to use.

 Don’t heat the holders! Only silicon disks can be heated

Ceramic disc: Ceramic disc are specifically for clay separations. The ceramic is porous and preferentially orientated the clay crystals. We currently have not developed an in-house sample preparation method for using the ceramic disc.  Creating our standard slurry and drying them in the desiccator would be ok. The preferred method is to dry using a vacuum system, which has not been currently developed on board. 

Aeris Setup

The mains power switch is on the rear lower right-hand side of the instrument. This can generally be left on. The unit is plugged in to the UPS power box and that should remain on at all times. Vendor recommends we leave the entire instrument and xray key switch on all the time.  If restarting is necessary to clear an error there is no need to toggle the key switch. Obviously for dry dock or when it’s totally necessary we can shut everything down, but it’s not good to be turned off and on often.

  • Make sure at least one sample holder spot is empty before turning on.
  • Turn the front computer on by pressing the power button on the right side of the screen. Let it initialize.  Sample changer arm should move and initialize.
  • Screen will prompt you to turn the key-switch, turn it clockwise and the "x-rays on" yellow lights around the instrument will light up. The screen goes to sleep when not in use, just move the mouse or touch the screen.
  • To turn off the instrument, press the power button on the side of the screen, and then toggle the key switch counter-clockwise.

Running a sample

  • Place sample into one of the six slots on the sample changer. Be careful not to touch the center arm that comes in and out of the shutter door.
  • Click on the MENU button in the top left of the screen and go to Measurement.
  • The 6 circles along the top of the screen correspond to the six sample slots.  Click on an active one to get started. (You can't click on one that is empty)
  • Select the appropriate measurement program in the dropdown.
  • Use the barcode scanner (on the right side of the Aeris) to scan the sample id label into the sample id field, or type it in with the keyboard. The file name will auto populate. Add any comments as necessary such as clay separation, heated, standard, test.
  • Click Start and the program will run right away. The screen changes to a live view of the scan in progress. If the sample is not in the sample changer you will not be able to click Start.
  • While the instrument is running the first sample, click on another circle where there is a sample and add the sample information and you can click "Add to Queue". 
  • When the sample has finished running, click on Next Measurement and you can add the next sample.



  • Once a sample is added to the Queue you cannot cancel it.  If you decide there is a mistake and you don't want to run a sample that has already been added to the queue, simply remove the sample from the sample changer. When the instrument gets to the empty slot it will show a warning that no sample is present and skip to the next sample.  Then you can place a sample back in the slot, click on the corresponding circle, and enter the new information.
  • You cannot enter any sample information into a slot that doesn't have a sample holder placed in it.  The sensor must sense a sample holder and then you will be able to add information and add it to the queue.

 If instrument is in Manual Mode: Due to the malfunctioning sample changer, the Aeris has been placed into "manual mode" by the service reps. You can bypass the sample changer and run one sample at a time by placing it gently on the center arm and then filling out the measurement fields on the screen as described above. The arm swings out of the chamber whenever the screen is activated, take care not to bump it. In this state, the screen permanently shows 1 active error "Motion control error on the sample changer gripper axis".

Uploading Data

When the scan is finished, the data file automatically transfers to the XRD lab computer and can be found in C:/ XRD Data. Create a new folder based on Expedition, Site, Hole to keep all the scans organized.

When you are ready to upload one or a batch of files, open MUT and under Options, go to Set Upload Directories and add the specific folder you want to upload. You may need to click Refresh so that MUT can find and display the files. Click Upload. Two file types, xrdml and Jpeg, are uploaded per sample. File name must be this format to be recognized and uploaded U1536B_5H3_79_81_CYL19622183

Importing a new measurement program

  • Open an existing file to edit or rename by clicking OPEN and navigate to C:/ PANalytical/XRDMP Creator/ . Make edits to the start and end angles and click Save As and rename for the current expedition. Save the creator file onto a USB drive. The USB can then be inserted into the side of the Aeris screen.
  • Click on the Menu button and select Advanced Mode. The password is panalytical
  • Click on Menu again and select Data Management. Then click Import Programs.
  • Source should auto populate as the USB drive. Select the program, click Import Program button.
  • Remove the USB drive and click Menu button to return to Measurement screen.

****PANalytical recommended measurement program settings are as follows (this is from on a document I found named AERIS_Suggested_Config.docx, from the factory/ installation)

Based on those data, I think the typical scan rate you will want to use is 40 sec/step (17min scan from 5 to 90 deg 2theta) and you might use a scan rate as slow as 200 sec/step for really challenging samples (or, as we discussed, repeat the scan at 40 sec/step five times and sum the results)

Bulk Samples

Scan Parameters

Start angle: 5 deg 2theta

End angle: 90 deg 2theta

Step Size: 0.0108664 deg 2theta

Time per step: 40 sec/step (longer as needed)

Incident (Tube) Side

Beta Filter: None

Soller Slits: 0.04 rad

Divergence Slit: ¼ deg

Beam Mask: 20mm

Sample Stage

Beam Knife: Beam Knife high

Spinner speed: 1 rps

Diffracted (Detector) Side

Anti-Scatter Slit: AS Slit 9mm

Soller slits: 0.04 rad

Beta Filter: Large beta filter Nickel


Type: PIXcel1D-Medipix3 detector

Mode: Scanning line detector (1D)

Active Length: 5.542 deg 2theta

PHD levels: Use defaults

Clay Speciation

Scan Parameters

Start angle: 2 deg 2theta

End angle: 30 deg 2theta

Step Size: 0.0108664 deg 2theta

Time per step: 40 sec/step (longer as needed)

Incident (Tube) Side

Beta Filter: None

Soller Slits: 0.04 rad

Divergence Slit: 1/16 deg

Beam Mask: 20mm

Sample Stage

Beam Knife: Beam Knife low

Spinner speed: 1 rps or NONE (if peaks seem broad because sample is wobbling)

Diffracted (Detector) Side

Anti-Scatter Slit: AS Slit 9mm

Soller slits: 0.04 rad

Beta Filter: Large beta filter Nickel


Type: PIXcel1D-Medipix3 detector

Mode: Scanning line detector (1D)

Active Length: 5.542 deg 2theta for fast (8 min) or 0.978 deg for slow (35 min) with better background

PHD levels: Use defaults

Very Low Angle Data

Scan Parameters

Start angle: 1 to 0.5 deg 2theta

End angle: 30 deg 2theta

Step Size: 0.0108664 deg 2theta

Time per step: 40 sec/step (longer as needed)

Incident (Tube) Side

Beta Filter: None

Soller Slits: 0.04 rad

Divergence Slit: 1/32 deg

Beam Mask: 20mm

Sample Stage

Beam Knife: Beam Knife low

Spinner speed: NONE (if peaks seem broad because sample is wobbling)

Diffracted (Detector) Side

Anti-Scatter Slit: AS Slit 9mm

Soller slits: 0.04 rad

Beta Filter: Large beta filter Nickel


Type: PIXcel1D-Medipix3 detector

Mode: Scanning line detector (1D)

Active Length: 0.5 to 0.109 deg 2theta (make the active length slightly smaller than ½ the start angle)

PHD levels: Use defaults

Creating A New Measurement Program

New measurement programs are created in XRDMP Creator.  Before creating a new program, use the excel file Aeris Setup Guide to choose proper configurations.  Start in the first tab, "Slit Guide" and enter the desired information such as start and end angles, and the diameter of the sample holder and the sheet will provide suggestions for recommended hardware options.  This is useful if wanting to use a sample holder with a different sized sample area.

Aeris Setup Guide.xlsx  Backup is located on the XRD instrument PC and in IODP Share > XRD

If starting off with one of the Panalytical predefined programs located in C: > Panalytical > XRDMP Creator > Panalytical Predefined Programs > Aeris, remember to only use the files marked Cu.  This indicates the setting are for a copper xray source which is what we have.  The Co indicates a cobalt source and we do not use that.

Original predefined programs are also backed up in IODP Share > XRD

Changing Hardware Configurations

Changing hardware is needed for a variety of reasons, low scan angles, size of sample holder, depth of sample,

In Advanced mode, select Manual Control, Unlock Cover.  Then lift the cover slowly until it stops on the ceiling. 

Use canned air to dust off any parts before inserting, the divergence slits tend to get dust in them. 

Beta Filter

Typically a beta filter is not needed on the source (tube) side.  Supplied is a Ni and Cu filter.  Ni filter may be used to run the Si standard blank for a system check.  If you do need to insert or remove this beta filter it should slide in an out completely freely without resistance and proper placement is sliding all the way in.  The writing will be facing the beam knife. 

Divergence Slit


You may need to change the divergent slit to run a low angle scan.  There is writing on both slides of the slit, but when looking at it from the side of the beam knife the writing will be right side up. In the picture above, the writing " 1/2 " appears upside down and this is correct.  Slide it in until the first small click.  It is possible to push it further and feel another click but that is too far and should be backed out. 

Beam Mask

Beam mask may need to be changed if the diameter of the exposed sample is different in different sample holders.  The writing should be facing the beam knife.  It should feel tight when inserting or removing, you need to put your finger in the opening to pull it out.  When inserting it should slide all the way down, no clicks or anything but you won't be able to push it too far. The picture on the right is what it looks like fully inserted.  

Beam Knife

Beam knife reduces air scatter and noise in the detector, it may need to be changed for low angle scans or system checks. 

Knife goes in the position you can read.

Beta Filter (detector side)

This filter should never need to be removed except when doing a Factory Acceptance Test or instructed to do so by PANalytical service techs for troubleshooting.  When sliding in and out it should slide freely.  When inserting you will feel a click in the middle and continue to push all the way in. 

Viewing and Analyzing Scans

Double click on any .xrdml file and the diffractogram will open in Data Viewer. This can be a quick and easy way to print and save the raw image. You can double click on more files and view the scans on top of each other. Click on the page icon, highlighted below, to view the complete report of parameters used in the scan. Scientists may want this information for their methods.

For peak identification and advanced processing use . See the HighScore Quick Start Guide.

Computer in XRD lab, smear slide and one in the computer lab have highscore installed.


The Aeris is provided with its own corundum standard (do not use the Bruker standard). It is a round white disk.  It should be kept in its sample holder to avoid getting scratched and damaged. Both corundum and the Si disk can be used to verify that the actual peaks align with theoretical peak angles.  Any drifting on the x-axis is uncommon for the Aeris and vendor recommends making any corrections to the x-axis in HighScore and not making any hardware or settings adjustments.  It is possible to change the system settings to correct this but only service technicians have access to that.

  • Run the corundum standard at the beginning, middle, and end of every expedition and compare to the original file in XRD Data > QAQC. 
  • Open the scans on top of each other in HighScore and they should line up exactly on top of each other.  Over time the peak intensities may reduce slightly and that is normal.  PANalytical service technicians advise that when to replace the x-ray tube is at our discretion if we feel the intensities are too low. 
  • If the scans do not line up you must figure out how much to correct the x-axis offset in HighScore and that must be done to any data files that might be affected. 
  • Email PANalytical service team that the x-offset must be corrected and they will be able to remote in to the instrument to make those corrections.  See Laboratory Notebook for service contact info.

SB: Jan 14, 2021: After service techs replaced sample changer and performed factory acceptance test during service call I created a measurement file C:/> PANalytical > XRDMP Creator > Corundum Standard Scan 5-120 deg.25 div SB.xrdmp and saved that file in C:/ > XRD Data > QAQC    The Aeris qaqc counts are lower then the brukers this is normal and due to higher resolution.  In order to make the counts higher increase the size of the divergence slits ( decreases resolution ) and increase run time.  The important part is the peaks position.

Original File backups are in Vol 1 > IODP Share > XRD > QAQC > Aeris

corundum 1_14_2021_SB.html

corundum 1_14_2021_SB.xrdml

Run the Si reference disk at least at the beginning, middle, and end of every expedition.  This tracks intensity and diminishes as the x-ray tube gets older.  Run it using the measurement program Aeris provided predefined creator program “Silicon (Cu Tube)”.  You need to unlock the cover and insert the ni filter if not already in.


Use a handheld vacuum to clean any dust inside or outside the instrument.

The bearings that spin the sample on the sample stage get dirty.  Clean them with isopropyl and a kim wipe.  If you notice residue on the rims of the sample holders it means these need to be cleaned.

Remove the panels: Put your hand in the recess on the panel and pull the panel away from the instrument.

Cooling Fluid: Check the cooling fluid level weekly. You can view and access the reservoir by opening the left rear panel. If the level is approaching the minimum limit then you must add more deionized water from the Barnstead dispenser in the chemistry lab.

  • Use a 6mm allen key to remove both the vent plug and fill plug.
  • Use the gooseneck refilling bottle to slowly add water into the fill plug up to the high mark. Do not overfill. Aeris does not need a lot of water.
  • Replace the fill plug and vent plug. Replace the side panel.
  • Aeris needs water added in the middle and end of each expedition at least.


Dust Filters: clean and vacuum at least once per expedition.  If they need replacing we have spares in the black PAnalytical XRD Service tool kit.  If you use the spares make sure sure to order another set.  In general keep the instrument clean and free of dust. 

Manufacturer recommends checking the safety system once per month:

This test is necessary to make sure that the HT keyswitch and safety loops work correctly and to move the related switches.

    1. Ma ke sure that the instru ment and HT generator are switched
    2. Turn the HT keyswitch counter-clockwise to switch off the

After 5 seconds, turn the HT keyswitch clockwise to switch on the HT

Advanced Mode

Click on the MENU icon and select Advanced Mode. PW: panalytical

In Advanced Mode the user can import and delete program files and delete old data that have already transferred to the PC.  In Manual Controls the user can unlock the cover if it is necessary to change any hardware or to inspect a problem and manually unload a sample that got stuck or lost. 

Select Minimize Window to gain access to the instrument computer.  Click the windows icon, and under Panalytical IMS select IMS Client. 

IMS Client:  Click on Scenarios, Run. This is where the user can backup the system files, troubleshoot network connection, and collect logs if needed to send to the vendor for servicing.  Some of the options are not available to us because you need a service dongle that PANalytical does not give out to their customers.  If further access is needed, the instrument must be given internet access by the MCS so that service techs can remote in to the instrument.

Backup the instrument system files and copy to a USB at least once per expedition. 

Network setup

See MCS.  Host computer is now online and no longer needs laptop connected for remote service calls.


Unfortunately, many troubleshooting options are only available to PAnalytical service techs.  They can access the instrument remotely to fix or diagnose issues, ask an MCS to give the instrument internet access to make this possible. 

Error codes: Some error codes can be cleared by turning off and back on the front computer. Press the power button on the side of the screen, do not turn the key switch. Wait a minute and Press the power button to turn back on.

Keyboard and mouse are wireless and run on batteries. If not working check the batteries and that the Bluetooth dongle is still in the Aeris, on the right hand side next to the network connections.

Files not exporting Error:

  • The first time the connecting wires came loose. Check the wires to make sure they are secure.
  • The data will not export to the computer if the network is down. See the MCS if there is a network issue.
  • After the instrument is turned off and back on the file transfer does not work and needs to be reconnected.
    • To be able to transfer files you will need to go to "Advanced Mode" password is "panalytical"
    • Once in "Advanced Mode" go to file, menu, and minimize screen
    • In the bottom right hand corner you will see a red "x". Click on this icon and it will open up the file. You will see "XRD Data"
    • Double click "XRD Data" file, it will open and reconnect itself.
    • The files will be able to be transferred again.
    • If the issue persists see the MCS.
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