Overview#

tomwer tomwer provides tools to automate acquisition and reconstruction processes for tomography. The suite includes:

  • Library Access: A library that allows users to access and manage each processing step individually.

  • GUI and Applications: User-friendly interfaces and standalone applications to control and execute main processes, such as reconstruction and stitching.

  • Orange add-on: An add-on for the Orange canvas to assist users in defining their workflows.

Be aware that some demo/tutorial videos are available on YouTube @tomotools.

To access it internally:

  1. Access resources

    From cluster-access:

    # A node to submit jobs to slurm (recommended)
salloc --partition interactive --x11 --mem=64G srun --pty bash -l
# A node with a GPU to do local reconstruction
salloc --partition gpu --x11 --gres=gpu:1 --mem=256G srun --pty bash -l

    or connect to visa on an instance with a GPU (recommended for training).

  2. Activate a Python environment with tomotools: Either using modules, for example:

    module load tomotools/{version}

    Version can be stable, dev, or a specific version like 1.4.

    When using the GUI, we encourage people to use the stable version.

  3. Launch tomwer:

    tomwer {command} {options}

    For example, to launch the canvas with a workflow file as a parameter:

    tomwer canvas my_file.ows

tomotools overview#

ecosystem

Projects scopes:

  • nabu: core processing

  • nxtomomill: convert raw data to NXtomo

  • nxtomo: read & write NXtomo

  • tomwer: provide GUI and allow workflow creation

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