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SIMPLI Manual

Installation

SIMPLI requires only Nextflow and Singularity and can be run immediately after cloning this repository. More installation details.

Inputs

SIMPLI works on highly multiplexed imaging data and performs analysis at the cell and pixel level, according to parameters specified in four metadata files. More information on input files.

Running SIMPLI

SIMPLI is run as a Nextflow pipeline from the command line. More details on running SIMPLI.

Outputs

Like its workflow SIMPLIs output can be divided in three main parts:

• Raw data extraction
• Image preprocessing and pixel level analysis
• Cell level analysis

Outputs from all three steps is described here.