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SIMPLI: Single-cell Identification from MultiPLexed Images

Documentation

Quick start

To try SIMPLI:

1. Install Singularity or Apptainer
2. Install Nextflow
3. Run either: nextflow run ciccalab/SIMPLI -profile test,singularity to use singularity nextflow run ciccalab/SIMPLI -profile test,apptainer to use apptainer

This will run SIMPLI on minimal example dataset distributed in this repository.

For more details on the example dataset and the associated analysis workflow see the example-workflow page.

Installing SIMPLI

SIMPLI can be installed just by cloning this repository to the desired location. For more details on installation and configuration see the installation page.

Running SIMPLI

SIMPLI is run as a Nextflow pipeline from the command line. For more a full documentation of SIMPLI parameters and configuration see the run page.

Inputs

SIMPLI works on highly multiplexed imaging data and can process input files in the following formats:

• Single-channel TIFF files.
• Multi-channel OME-TIFF files.
• TXT acquisition files from Imaging Mass Cytometry experiments.
• MCD acquisition files from Imaging Mass Cytometry experiments.

For more information on input files, see the input page.

Analysis Workflow

The workflow of SIMPLI is highly configurable and the user can select which steps to run to create ad-hoc workflows.
The input, output and options of each step of the analysis are described in the analysis page.

Ad-hoc CellProfiler4 Pipelines

SIMPLI can use CellProfiler4 pipelines for two analysis steps:

• Image preprocessing.
• Cell segmentation and single-cell measurements.

Both steps can be highly customized for the specific requirements of each analysis with user-defined pipelines. For the full documentation of the design of ad-hoc CellProfiler4 pipelines compatible with SIMPLI please refer to the CellProfiler4 pipelines page.

SIMPLI: Single-cell Identification from MultiPLexed Images