SpicyR: Spatial analysis of in situ cytometry data
Analysis
Example
Upload Spatial (Segmented Cells) data. Choose csv file
Browse...
Upload Phenotype data. Choose csv file
Browse...
Segmented Cell Column
Select imageID (Required)
Select X & Y coordinates (Required)
Select cellType (Required)
Assign Segmented Cell columns
Finished assigning segmented cell columns?
Phenotype Column
Select imageID (Required)
Select Condition (Required)
Select Subject (Optional)
Select Covariates (Optional)
Assign Pheonotype columns
Finished assigning phenotype columns?
Example
Choose attribute to display
Segmented Cell Data
Phenotype Data
Visualise Spatial Distribution?
Plot distribution for imageID:
Example
Calculate specific interactions?
from
to
Bootstrapping?
Choose number of bootstrap samples?
Include image specific variance weights?
Run spicy?
P-value threshold
Generate Report
Dataset
Data Summary
Perform spicy analysis