Basis to perform a microtomography experiment at ID19

2 instruments are available on ID19 for microtomography:
- 1 for High Resolution from 0.28 to 2.8 microns (Microtomo HR)
- 1 for Medium Resolution from 5 to 30 microns (Microtomo MR)
 

UPPER PART OF ID19 HIGH RESOLUTION MICROTOMOGRAPH
	Abbreviations... WB: White Beam MB: Monochromatic Beam MT: MicroTomograph PS: Primary Slits SS: Secondary Slits AS: Accurate Slits VO: Vertical Offset HO: Horizontal Offset VG: Vertical Gap HG: Horizontal Gap HR: High Resolution MR: Medium Resolution
From bottom to up: thx, pmy, pmo, sbx and sby

 

Motor mnemonic	Role	Limit - (mm)	Limit + (mm)
z0	General z motion (sample+camera)	-10.1	149
thy	rotation axis parallel to middle camera column (alignxc)	-0.15	2.1
thz	xc translation parallel to beam (alignxc)	0.4	-0.4
zc	camera z motion (usually near 0)	-7.5	32
yc	camera y motion yc=0 to use MT yc=100 to use other further instruments	-20.5	100
xc	camera x motion = sample/detector distance	6	1000.1
focus	distance first lens/scintillator	HR -0.5 LR -45	HR 0.5 LR 45
thx	rotation axis perpendicular to the beam - replaced by rotc At the moment, 90º turned for topotomo experiment	-2.1	2.1
rotc	rotation axis in the middle column of the ccd At the level of the camera (alignment)	-2.1?	2.1?
pmo	sample rotation from 0 to 180º	-1	181
pmy	rotation axis translation: usually around -4mm (alignment)	75	-75
sbx	sample positionning at 90º	-5	5
sby	sample positionning at 0 and 180º	-5	5
sz	z sample positionning	-30	10

 

 

 

WHO...	HOW TO...
Local contact	Experimental setup
Local contact	FOCUS setup for FReLoN
Local contact	Beam alignment (alignxc) only for HR microtomograph
Local contact	Rotation axis alignment (alignment)
Users	Sbx and sby positionning for each sample

 

Experimental setup

Different setups are available on ID19 (topography, tomography, laminography, ...)

 

 

 

 

 

Check diamond Undulator/Wiggler
Adjust slits to your beam size
Select (at least) camera optics used with ftomo> ftomosetup to have correct image orientation
Use: "print_energy" SPEC macro on Ganymedes in any SPEC session to know actual setup. "set_energy" SPEC macro on Ganymedes in any SPEC session to select needed energy with actual setup. "change_setup" SPEC macro on Ganymedes in any SPEC session to select needed setup.
VMONO			Multilayer (3 bands)
For energy>30 keV put a filter in att SPEC session 30keV 1mm Al 40keV 2mm Al			For energy>15 keV put a filter in att SPEC session 15keV 0.5mm Al 30keV 1mm Al 40keV 2mm Al
Check focus
Put your sample and check the working energy (= check transmission)
			Run SPEC 'alignxc' macro
Run SPEC 'alignment' macro
Put your sample and make sbx and sby positionning
Run ftomosetup macro to set scan parameters
Run fasttomo scan
It's NOT necessary to realign when changing energy			It's NECESSARY to realign when changing energy !!!!

 

 

FOCUS setup for FReLoN

To find the best focus position, run:

ftomo> dofocus
Do you want to put the paper in the beam? Y (this is to give contrast for focus optimization)

Do you want to remove the paper? Y

The principle is to put an object in the beam that gives contrast. Average and standard deviation are measured on several images, ie at several focus positions. Focus is automatically set at the maximum position, but no set 0 on the motor is applied.

 

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Alignxc (thy and thz)

This alignment consists in putting xc translation, parallel to the beam, by recording several images at different sample/detector distances.

1) Run alignxc 1 SPEC macro. Camera will move from xc=100mm to xc=900mm
Images are automatically saved in a special directory.
2) Move thy and thz to the OCTAVE calculated values.
3) Run alignxc -1 SPEC macro. Camera will move from xc=900mm to xc=100mm
4) Redo alignxc up to obtain values better than 0.001º
5) Put your original xc position

 

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Alignment (rotc and pmy)

This alignment consists in putting the rotation axis exactly (rotation with rotc and translation with pmy) in the middle column of the CCD.

1) Put a needle or a tungsten wire into the beam to simulate rotation axis
2) Enter correct values for sample displacement and exposure time in ftomosetup SPEC macro
3) Run alignment SPEC macro
4) Move rotc and pmy to the OCTAVE calculated values
5) Redo alignment up to obtain values better than 0.01º for rotc and less than one pixel for pmy

 

alignment is alignment 1 by default

 

to adjust only pmy with your sample, use alignment -1

 

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sbx and sby positionning to do for each new scan

This positionning consists in adjusting the sample in regards of the rotation axis (thanks to sbx and sby translation motors)

1) Put the sample on the support, without applying any constraint which could damage the alignment ! ! !
2) Procedure to close the experimental hutch
3) Open Variable Beam Shutter
ftomo> shopen
4) Check the sample position with regard to rotation axis
Check motor positions with this command :
ftomo> wu (‘wu’ for watch user values)
We suppose that the pmo rotation is in 0º position (normal position at the end of the previous scan).
Acquire an image:
ftomo> ct 0.3 (‘ct’ for count)
Sample must be in the field of view. Center it using sy
(See joined diagram for moving sense).
Example : ftomo> mvr sby 0.2 (value in mm)

Make a rotation of 90°:
ftomo> mvr pmo 90 (90° relative movement of pmo motor)
Acquire an image at this position (90°) to check that you can see the whole sample :
ftomo> ct 0.3
If necessary, center sample using sx motor
(See joined diagram for moving sense).
Example : ftomo> mvr sbx 0.2 (value in mm)

 

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BE CAREFUL : NEVER DO mvr pmo 180 or mvr pmo –180 because pmo motor is clever. It chooses the shorter way to make the asked rotation and it may choose a rotation which corresponds to 360° ! ! ! (and BING in the camera ! ! ! !)

 

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5) Come back to 0º position
ftomo> mvr pmo –90

6) The sample is now well situated with regard to the rotation axis
The image acquisition can begin.
Set up of the parameters which will allow the automation of the acquisition and the future reconstruction:
ftomo> ftomosetup
Answer these questions:
Energy (keV)
Sample-detector distance (mm)
Number of images in the scan
Exposure time for each image [s]
Intermediate reference images after n projections
Number of reference images to average
Number of dark images summed
Sample displacement (mm)
Directory where to save images /data/id19/external/yyyy (yyyy is the name of your experiment)
Optic used

7) Check that the 3 panels are light on
For their meaning, see here.

8) Run the acquisition

180 degrees mode

ftomo> fasttomo scan_name
The automatic acquisition begins…
This following directory will be automatically created: /data/id19/external/yyyy/scan_name
Images will be saved in this directory with this form: scan_name0000.edf (‘.edf’is the ESRF image format)
Reference images (=beam images without sample) and dark images will be also saved.

 

 

360 degrees mode

 

 

ftomo> fasttomo360 scan_name

9) When the acquisition is finished or even during dark images:
Open the hutch and let's start with the next sample…
If you want to reconstruct one slice, see the following page.