# Using squidpy following scRNAseq and spatialRNASeq integration with scanorama and scanpy

**URL:** <https://discourse.scverse.org/t/using-squidpy-following-scrnaseq-and-spatialrnaseq-integration-with-scanorama-and-scanpy/3433>\
**Category:** Help\
**Created:** [January 17, 2025, 7:40pm UTC](https://discourse.scverse.org/t/using-squidpy-following-scrnaseq-and-spatialrnaseq-integration-with-scanorama-and-scanpy/3433 "2025-01-17T19:40:30Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![gme](https://avatars.discourse-cdn.com/v4/letter/g/5fc32e/32.png) [@gme](https://discourse.scverse.org/u/gme)\
**Post date:** [January 17, 2025, 7:40pm UTC](https://discourse.scverse.org/t/using-squidpy-following-scrnaseq-and-spatialrnaseq-integration-with-scanorama-and-scanpy/3433/1 "2025-01-17T19:40:30Z")

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Hi, I integrated scRNAseq and spatialRNASeq data using the scanpy tutorial. [Integrating spatial data with scRNA-seq using scanorama — scanpy](https://scanpy.readthedocs.io/en/stable/tutorials/spatial/integration-scanorama.html) However, when trying to compute distance between these clusters using squidpy it does not work. [Analyze Visium H&E data — squidpy documentation](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_visium_hne.html) Do you know how we could fix it by any chance ? Thank you Guillaume