Tomography scans are managed by tomoScan, a tomography scanning engine developed by Mark Rivers from GSE-CARS and Francesco DeCarlo from the Imaging group to control tomography data acquisition.

Starting tomoscan

The tomography scans are managed by tomoScan. Please refer to the tomoScan documentation for details.

To configure a single tomographic scan enter the acquistion parameters at:


To run a single scan with the parameters set in the tomoScan screen press the green Start Scan button. To collect the same from the command line interface:

[user@workstation]$ tomoscan single

tomoscan supports also vertical, horizontal and mosaic tomographic scans with:

[user@workstation]$ tomoscan vertical
[user@workstation]$ tomoscan horizontal
[user@workstation]$ tomoscan mosaic

to run a vertical scan:

$ [user@workstation]$ tomoscan vertical --vertical-start 0 --vertical-step-size 0.1 --vertical-steps 2

2020-05-29 16:54:03,354 - vertical scan start
2020-05-29 16:54:03,356 - vertical positions (mm): [0.  0.1]
2020-05-29 16:54:03,358 - SampleInY stage start position: 0.000 mm
2020-05-29 16:54:03,362 - single scan start
2020-05-29 16:54:51,653 - single scan time: 0.805 minutes
2020-05-29 16:54:51,654 - SampleInY stage start position: 0.100 mm
2020-05-29 16:54:51,658 - single scan start
2020-05-29 16:55:47,607 - single scan time: 0.932 minutes
2020-05-29 16:55:47,607 - vertical scan time: 1.738 minutes
2020-05-29 16:55:47,608 - vertical scan end

to run a series of vertical scans starting from different locations:

[user@workstation]$ for k in {0,5.2,10.4,15.6,20.8,26}; do tomoscan vertical --vertical-start $k --vertical-step-size 1.3 --vertical-steps 4; done

this will run:

[user@workstation]$ tomoscan vertical --vertical-start 0 --vertical-step-size 1.3 --vertical-steps 4
[user@workstation]$ tomoscan vertical --vertical-start 5.2 --vertical-step-size 1.3 --vertical-steps 4
[user@workstation]$ tomoscan vertical --vertical-start 10.4 --vertical-step-size 1.3 --vertical-steps 4
[user@workstation]$ tomoscan vertical --vertical-start 15.6 --vertical-step-size 1.3 --vertical-steps 4
[user@workstation]$ tomoscan vertical --vertical-start 20.8 --vertical-step-size 1.3 --vertical-steps 4
[user@workstation]$ tomoscan vertical --vertical-start 26 --vertical-step-size 1.3 --vertical-steps 4

please check the command line manual for more details.

Raw Data Viewer

To view the tomographic raw data we suggest to install Fiji and add this HDF plugin.

Other options are hdfview or argos.