Alternative Mapping Methods - CytoSpace and Tangram
STellaris implements several public computational methods in the step of spatial mapping, such as CellTrek (https://github.com/navinlabcode/CellTrek), Tangram (https://github.com/broadinstitute/Tangram) and CytoSPACE (https://github.com/digitalcytometry/cytospace), to ensure the versatility of the web server.
Here, we implemented Tangram and recently published CytoSPACE as alternative options on our web server.
- Tangram
As an example, we applied Tangram method to the three case studies in the manuscript:
- Case study 1: Mouse fetal brain (https://spatial.rhesusbase.com/mapping/resultPage/0d87b0b0-e279-11ed-a7be-d5203751b098)
- Case study 2: Human squamous cell carcinoma (https://spatial.rhesusbase.com/mapping/resultPage/dfe37db0-e345-11ed-a152-c54e6b856dd2)
- Case study 3: H3K4me3 modification in mouse brain (https://spatial.rhesusbase.com/mapping/resultPage/be0f8ac0-e599-11ed-9827-4d92302fbdb4)
The results are approximately consistent with those based on CellTrek strategy.
- CytoSPACE
As an example, we applied CytoSPACE method to the three case studies in the manuscript:
- Case study 1: Mouse fetal brain (https://spatial.rhesusbase.com/mapping/resultPage/98ef1750-df5a-11ed-adc4-89347291db6a)
- Case study 2: Human squamous cell carcinoma (https://spatial.rhesusbase.com/mapping/resultPage/b9ed1440-df85-11ed-8a5b-0367168fe5ce)
- Case study 3: H3K4me3 modification in mouse brain (https://spatial.rhesusbase.com/mapping/resultPage/fea07ba0-c300-11ed-a279-53f5a82d6e80)
We found that the conclusions are consistent with those based on CellTrek strategy.
In the future, we will continue to integrate new spatial mapping tools into our web server and add new options to the workflow.