Table 1.
Overview of various image analysis tools.
| Package | Type | Suited for Ca imaging | 3D calcium imaging | Motion correction | ROI extraction | Project management | ROI annotation | Temporal annotation | Sample annotation | Graphical interfaces | Scripting interfaces | Downstream analysis | FAIR dataset creation | Visualization | Interactive visualization |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mesmerize | Platform | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Caiman | Pipeline | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | L | ✓ | ✗ | ✗ | ✗ | ✗ |
| Suite2p | Pipeline | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | L | ✓ | L | ✗ | L | ✗ |
| EZCalcium | Pipeline | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | L | ✗ | ✗ | ✗ | ✗ | ✗ |
| SIMA | Pipeline | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | L | ✓ | ✗ | ✗ | ✗ | ✗ |
| S. A Romano | Pipeline | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | L | L | L | ✗ | L | ✗ |
| SamuROI | GUI Tool | ✓ | L | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | L | L | ✗ | ✗ | ✗ | ✗ |
| DataJoint | Workflow management | ✓ | ✓ | ✗ | ✓ | ✗ | ✓ | ✓ | L | ✓ | ✓ | ✓ | ✗ | ✗ | |
| OMERO | Platform | ✗ | ✗ | ✗ | ✓ | ✓ | L | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ |
| Biaflows | Platform | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | L | ✓ | ✓ | L | ✓ | ✗ | ✗ |
| Cytomine | Platform | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ |
| openBIS | Platform | ✗ | ✗ | ✗ | ✓ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ |
| KNIME | Platform | ✗ | ✗ | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✓ | ✓ | ✓ | ✗ | ✗ |
An overview of various tools for calcium imaging analysis and dataset organization. The availability of various features for calcium imaging analysis, data annotation, data management, analysis, and visualization are shown (Available: ✓; Limited availability: L; Not available: ✗).