What to know/do before starting tomo experiment

Two instruments are available on ID19 for microtomography:

- 1 for High Resolution from 0.16 to 1.6 micron (Microtomo HR)

- 1 for Medium Resolution from 2.2 to 50 microns (Microtomo MR)

UPPER PART OF ID19 HIGH RESOLUTION MICROTOMOGRAPH
	Abbreviations... PB: Pink Beam MB: Monochromatic Beam MT: MicroTomograph PS: Primary Slits SS: Secondary Slits VO: Vertical Offset HO: Horizontal Offset VG: Vertical Gap HG: Horizontal Gap HR: High Resolution MR: Medium Resolution
From bottom to up: sz, yrot , srot, sx and sy

FOCUS setup for camera

To find the best focus position, run:

XXtomo> 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.

Alignxc (thy and thz) only for HR instrument

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

Alignment (rotc and yrot)

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

1) Put a needle or a tungsten/cupper 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 yrot to the OCTAVE calculated values
5) Redo alignment up to obtain values better than 0.01º for rotc and less than one pixel for yrot

alignment is alignment 0 by default

to adjust only yrot with your sample, use alignment 2

sz, sx and sy positionning to do for each new scan

This positionning consists in adjusting the sample in regards of the rotation axis (thanks to sx and sy 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 srot 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 sy 0.2 (value in mm)

Make a rotation of 90°:
ftomo> mvr srot 90 (90° relative movement of srot motor)
Image is acquired automatically after a movement (option updateon/updateoff)

If necessary, center sample using sx motor
(See joined diagram for moving sense).
Example : XXtomo> mvr sx 0.2 (value in mm)

5) 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:
XXtomo> ftomomenu

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

7) Run the acquisition

180 degree mode (more details)

XXtomo> fasttomo scan_name_

(_ at the end of the name is mandatory!!!)

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

360 degree mode (more details)

XXtomo> fasttomo360 scan_name_

8) 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.

Insitu mode

XXtomo> insitutomo scan_name_ number_of_scans interval_between_scans [first_scan_number]