Performance Test

Stereo-seq Test Data

Sample	Cell Number	Cell Types (n)
sample1_bin100	17,884	29
sample1_bin50	70,761	38
sample1_bin20	439,383	39
sample1_cellbin	134,703	39
sample2_bin100	23,061	11
sample2_bin50	91,106	11
sample2_bin20	5,643,322	11

Runtime and Memory Usage

• Squidpy: Both runtime and memory usage increase with the number of cells. For different bin sizes, the runtime is typically less than 1 hour. However, memory usage increases significantly for bin20.

• CRAWDAD: Runtime and memory usage also increase with the number of cells. For different bin sizes, memory usage generally remains below 10 GB, but runtime increases significantly for bin20.

• CRAWDAD: The runtime is highly sensitive to the value of --crawdad_perms. Increasing this parameter improves the accuracy of p-values but also substantially increases computation time. The default value is 10.