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Example Workflow
MicheleBortol edited this page Apr 19, 2021
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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/.