Table 2.
Description of the case studies used to test SIMPLI.
| Case study | Imaging technology | Analysed samples (n) | Channels (n) | ROI (mm2) | Resolution (µm/pixel) | HPC platform | CPU time (h) | Elapsed real time (h) | RAM (GB) | Processes |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 (Fig. 2) | IMC | 6 | 28 | 1.00 | 1.00 | SGE | 00:20:41 | 00:06:10 | 4.1 |
Raw data processing Cell masking Single-cell quantification Pixel intensity comparison |
| 2 (Fig. 3) | IMC | 1 | 28 | 1.00 | 1.00 | SLURM | 00:06:25 | 00:05:30 | 4.2 |
Raw data processing Cell masking Unsupervised clustering Expression thresholding Homotypic cell distances |
| 3 (Fig. 4) | mIF | 1 | 7 | 5.45 | 0.50 | SLURM | 00:11:45 | 00:08:23 | 16.7 |
Thresholding and masking Expression thresholding Heterotypic cell distances |
| 4 (Fig. 5) | CODEX | 35 | 58 | 1.13 | 0.38 | SGE | 02:32:35 | 00:26:01 | 22.5 |
Expression thresholding Heterotypic cell distances |
For each case study, listed are the imaging technologies used to generate the tissue images, the number of samples and markers used, the size of the analysed region of interest (ROI), the resolution of the obtained images, the high-performance (HPC) platform and the computational resources employed to perform the analysis. These include the central processing unit (CPU) time and the elapsed real time, as well as the maximum random access memory (RAM) memory used. Finally, the specific analytical processes performed in each case study are also listed (single-cell segmentation was performed in all of them).
SGE Sun Grid Engine, SLURM Simple Linux Utility for Resource Management.