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Example Workflow
Each installation of SIMPLI includes a self-containe example/test dataset and all the metadata and configuration files required for its analysis.
The example dataset provided with SIMPLI consists of two Imaging Mass Cytometry derived images of normal colon mucosa. The images are derived from the ablation of two ROIs from two different FFPE blocks from two individuals who underwent surgery for the removal of colorectal cancers.
The two example images contain the channels, with the intensities associated to this panel of metal conjugated antibodies.
| Metal | Marker | Target Cells / Features |
|---|---|---|
| Ir191 | DNA1 | All nucleated cells |
| Sm152 | CD45 | All leukocytes |
| Yb173 | CD45RO | T cells |
| Er166 | CD45RA | T cells |
| Er170 | CD3 | T cells |
| Dy162 | CD8a | T cells |
| Ho165 | PD1 | T cells |
| Gd156 | CD4 | T cells, Macrophages |
| Gd155 | FoxP3 | T cells |
| Yb171 | CD27 | B cells, T cells |
| Dy161 | CD20 | B cells |
| Pr141 | IgA | B cells |
| Tm169 | IgM | B cells |
| Tb159 | CD68 | Macrophages |
| Nd146 | CD16 | Macrophages |
| Lu175 | CD11c | Macrophages, Dendritic cells |
| Nd150 | PDL1 | Macrophages, Dendritic Cells |
| Nd148 | PanKeratin | Epithelial Cells |
| Gd158 | eCadherin | Epithelial Cells |
| Er168 | Ki67 | Proliferating cells |
| Nd143 | Vimentin | Stromal cells |
| Dy164 | CD34 | Endothelial cells |
| Nd142 | SMA | Smooth muscle |
| Yb176 | CollagenIV | Basement membrane cells |
| Yb174 | CAMK4 | Various |
| Sm154 | VEGFc | Various |
| Sm147 | IFNA5 | Various |
The raw images files used in SIMPLI's example workflow are two .txt IMC acquisition files with one Region Of Interest (ROI) each. These files are available in SIMPLI's repository and in your local SIMPLI installation folder: SIMPLI/test/raw_data/.
The metadata and configuration files required for running an analysis of the example dataset are stored at SIMPLI/test/ and include:
- Configuration file with all the parameters for running SIMPLI.
- CellProfiler4 pipelines for image preprocessing and cell-data extraction.
- Metadata files for each step of the analysis.
The most recent version of SIMPLI be downloaded and run from directly from this repository with:
nextflow run https://github.com/ciccalab/SIMPLI -profile test
In alternative the example analysis can be run from an existing installation of SIMPLI with:
nextflow main.nf -profile test