CLI

Command-line interface

Some of the functions from LuTuFlow can be run from the terminal via the command-line interface.

⚠️ The CLI is only available when the software is installed as a Python package.

You can run LuTuFlow in batch and interact with OMERO projects. For more details, see lutuflow omero --help.

You can run the tumor detection workflow from the terminal on an OMERO project. Find the OMERO project ID, then run the command:

lutuflow omero run <project_id>

You can start the CLI in interactive mode using the command:

lutuflow omero interactive

Interactive mode

The functionalities available in this interactive mode include:

Run detection workflow
Upload new scans in batch
Select a cases and download them locally (including the rois_timeseries.tif and tumors_untracked.tif)

Run a YoloV8 model to segment the lungs cavity and crop the image around the lungs.

lutuflow crop <image_file> <out_dir>

For more details, see lutuflow crop --help.

Run a nnUNet model to segment tumor nodules.

lutuflow predict <image_file> <out_dir>

For more details, see lutuflow predict --help.

Combine several 3D images (ZYX) into a single 4D image (TZYX).

lutuflow combine <image_1> <image_2> <image_3> <out_dir>

For more details, see lutuflow combine --help.

Track tumor nodules across a 4D mask (TZYX) time series using laptrack.

lutuflow track <labels_file> <image_file>

For more details, see lutuflow track --help.

lutuflow serve --port 8000

Create an Imaging Server Kit server to use LuTuFlow functions remotely.

For more details, see lutuflow serve --help.