Overview¶

tomwer tomwer is offering tools to automate acquisition and reconstruction processes for Tomography. It contains:

  • a library to access each acquisition process individually
  • gui and applications to control main processes (reconstruction, data transfert...) and execute them as a stand alone application.
  • an orange add-on to help users defining their own workflow (http://orange.biolab.si)

Be aware that some demo/tutorial videos are available on https://www.youtube.com/@tomotools

To access it internally

  1. access ressources

From cluster-access:

# a node to submit job to slurm (recommanded)
salloc --partition interactive --mem=64G srun --pty bash -l
# a node with a gpu to do local reconstruction
salloc --partition gpu --gres=gpu:1 --mem=256G srun --pty bash -l

or connect to visa on a instance with a gpu (recommanded way for the training)

  1. activate a python environment with tomotools: Either using 'modules' like
module load tomotools/{version}

or from the activate.sh script like:

source /scisoft/tomotools/activate {version}

version can be dev, stable, 1.0 for example. When using the GUI we encourage people to use the 'stable' version. For this training we will use the training_2024 version. Which contains software about to be released.

  1. launching tomwer
tomwer {command} {options}

like to launch the canvas with a workflow file as a parameter:

tomwer canvas my_file.ows
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