# Conduct SCANVI after running SysVI on multi-platform data

**URL:** <https://discourse.scverse.org/t/conduct-scanvi-after-running-sysvi-on-multi-platform-data/3745>\
**Category:** scvi-tools\
**Created:** [August 2, 2025, 8:40pm UTC](https://discourse.scverse.org/t/conduct-scanvi-after-running-sysvi-on-multi-platform-data/3745 "2025-08-02T20:40:30Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![coarfa](https://avatars.discourse-cdn.com/v4/letter/c/bbce88/32.png) [@coarfa](https://discourse.scverse.org/u/coarfa)\
**Post date:** [August 2, 2025, 8:40pm UTC](https://discourse.scverse.org/t/conduct-scanvi-after-running-sysvi-on-multi-platform-data/3745/1 "2025-08-02T20:40:30Z")

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Hi,

I really appreciate the power of SysVI to correct large batch effects between different platforms. Once SysVI has been run between a reference on one platform and an unnanoted dataset on a second platform, how can we run SCANVI to conduct cell type labeling?

Thank you

Cristian

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**Author:** ![cane11](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/cane11/32/241_2.png) [@cane11](https://discourse.scverse.org/u/cane11)\
**Post date:** [August 2, 2025, 9:56pm UTC](https://discourse.scverse.org/t/conduct-scanvi-after-running-sysvi-on-multi-platform-data/3745/2 "2025-08-02T21:56:43Z")

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Hi, this is not supported and would require actually establishing the model, e.g. cycle-consistency loss should be guaranteed to provide same cell-type label. However, you can run a simple kNN classifier in latent space as done in our tutorials to perform cell-type transfer, see e.g. [https://www.biorxiv.org/content/10.1101/2024.09.19.613883v3](https://www.biorxiv.org/content/10.1101/2024.09.19.613883v3)

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<div class="post-metadata">

**Author:** ![coarfa](https://avatars.discourse-cdn.com/v4/letter/c/bbce88/32.png) [@coarfa](https://discourse.scverse.org/u/coarfa)\
**Post date:** [August 3, 2025, 12:10am UTC](https://discourse.scverse.org/t/conduct-scanvi-after-running-sysvi-on-multi-platform-data/3745/3 "2025-08-03T00:10:34Z")

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Thank you very much, will try knn since sysVI did a much better job of integrating the datasets than anything else I tried.

Best regards

Cristian

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<div class="post-metadata">

**Author:** ![cane11](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/cane11/32/241_2.png) [@cane11](https://discourse.scverse.org/u/cane11)\
**Post date:** [August 3, 2025, 4:34pm UTC](https://discourse.scverse.org/t/conduct-scanvi-after-running-sysvi-on-multi-platform-data/3745/4 "2025-08-03T16:34:52Z")

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For completeness, [Querying the Human Lung Cell Atlas — scvi-tools](https://docs.scvi-tools.org/en/1.3.3/tutorials/notebooks/hub/query_hlca_knn.html) provides a tutorial for a kNN classifier.