BEATS Computing Infrastructure

DAQ workstation - BEATS-control-ws

The data acquisition (DAQ) workstation is used to control the beamline and scan settings. Visit the section Data Acquisition (DAQ) for more information.

Useful commands

Mount PETRA:

sudo mount -t nfs 10.1.14.100:/PETRA/SED/BEATS/IH /PETRA/SED/BEATS/IH

SMB mount of SSCAN data folder:

sudo mount -t cifs -o vers=3,username=beats.smb '\\10.1.14.100\pco-flir-ws' /home/control/Desktop/SSCAN

Start the Energy GUI:

cd /home/control/energy/iocBoot/iocEnergy_2BM
python3 -i start_energy.py

Data analysis workstation - BL-BEATS-WS01

The data analysis workstation is used for several purposes including:

• Inspection of sinograms and CT reconstruction

• Submit reconstruction jobs on the cluster rum@sesame.org.jo

• 3D image visualization and processing

The list of software available on the workstation is listed in the section on :ref:’Data analysis software’ below.

Useful commands

Start alrecon CT reconstruction environment:

conda activate tomopy
solara run alrecon.pages --host localhost

Start reconstruction pipeline on Jupyter Lab. Available pipelines are described in section Tomographic reconstruction at BEATS:

conda activate tomopy
jupyter lab

Mount proposal ExpData and recon folders on BL-BEATS-WS01:

cd ~
./petra_prop_mounter.sh

Check mount points:

df -h

Unmount proposal folders:

umount /PETRA/SED/BEATS/SEM_6/20235010
umount /PETRA/SED/BEATS/SEM_6_recon/20235010

Mount proposal ExpData and recon folders on Win Data Dispenser and Dragonfly VizServer:

./petra_prop_recon_smb_mounter.sh

Note

For proposals belonging to a different semester the scripts petra_prop_mounter.sh and petra_prop_recon_smb_mounter.sh must be modified.

Data analysis software

The software in the table below can be used to inspect and process 3D image data (sinograms and CT reconstructions) at SESAME BEATS.

Name	URL	Open source	Features
ImageJ	https://fiji.sc/	yes	Essential for data collection and reconstruction
Paraview	https://www.paraview.org/	yes	3D image rendering
Dragonfly	https://www.theobjects.com/dragonfly/index.html	no	3D image analysis and visualization
3D Slicer	https://www.slicer.org/	yes	3D image analysis and visualization
TomoPy	https://tomopy.readthedocs.io/en/stable/	yes	CT reconstruction in Python
Alrecon	https://github.com/gianthk/alrecon/tree/master	yes	Web app for CT reconstruction
Jupyter	https://jupyter.org/	yes	Interface for Python reconstruction pipelines (notebooks)

Load reconstructed volume with ImageJ

Reconstructions at SESAME BEATS are generally saved as a stack of .TIFF images contained in a reconstruction folder. To load a reconstruction in ImageJ use the command File › Import › Image Sequence. You can follow this video for a detailed explanation on how to import image sequences.

Note

Always select the option Use Virtual Stack when you import large image stacks in ImageJ!

rum - BEATS reconstruction cluster

Access the reconstruction cluster rum@sesame.org.jo with:

ssh -X beatsbs@rum.sesame.org.jo

Data dispenser PC

Dragonfly VizServer

SESAME data portal