# \#integration

**URL:** https://discourse.scverse.org/tag/integration/3.md

[Latest](https://discourse.scverse.org/latest.md) · [Categories](https://discourse.scverse.org/categories.md) · [Tags](https://discourse.scverse.org/tags.md)

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## [Can scVI take as input SCT-normalized data?](https://discourse.scverse.org/t/can-scvi-take-as-input-sct-normalized-data/4042)

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**Author:** [@gboscagli](https://discourse.scverse.org/u/gboscagli)\
**Replies:** 2\
**Last updated:** [September 8, 2026, 8:53am UTC](https://discourse.scverse.org/t/can-scvi-take-as-input-sct-normalized-data/4042 "2026-09-08T08:53:42Z")

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Hi all, i am trying to perform scVI integration on a merged dataset processed in R and normalized with scTransform. I want to use native Python implementation rather than Seurat wrapper, since i want to play around with…

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## [Open-source pipeline for integrating spatial transcriptomics and proteomics in 3D microscopy](https://discourse.scverse.org/t/open-source-pipeline-for-integrating-spatial-transcriptomics-and-proteomics-in-3d-microscopy/4046)

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**Author:** [@yumin-lian](https://discourse.scverse.org/u/yumin-lian)\
**Replies:** 0\
**Last updated:** [September 4, 2026, 9:33pm UTC](https://discourse.scverse.org/t/open-source-pipeline-for-integrating-spatial-transcriptomics-and-proteomics-in-3d-microscopy/4046 "2026-09-04T21:33:24Z")

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We developed a machine-learning-aided analysis pipeline for highly multiplexed spatial transcriptomics and proteomics data from mouse brain tissue. The pipeline integrates image processing, 3D registration, cell/nucleus …

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## [Allowed downstream analysis with get\_normalized\_expression?](https://discourse.scverse.org/t/allowed-downstream-analysis-with-get-normalized-expression/4039)

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**Author:** [@gboscagli](https://discourse.scverse.org/u/gboscagli)\
**Replies:** 6\
**Last updated:** [July 30, 2026, 9:06am UTC](https://discourse.scverse.org/t/allowed-downstream-analysis-with-get-normalized-expression/4039 "2026-07-30T09:06:34Z")

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Greetings all, Hope I won’t be redundant with this issue. I am interested in finding an integration tool which returns a full gene-space batch-corrected matrix to use for downstream analysis, and I bumped into scVI’s g…

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## [SCVI view\_anndata\_setup causes AttributeError with rich.pretty](https://discourse.scverse.org/t/scvi-view-anndata-setup-causes-attributeerror-with-rich-pretty/4022)

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**Author:** [@ggruenhagen3](https://discourse.scverse.org/u/ggruenhagen3)\
**Replies:** 1\
**Last updated:** [July 8, 2026, 6:45am UTC](https://discourse.scverse.org/t/scvi-view-anndata-setup-causes-attributeerror-with-rich-pretty/4022 "2026-07-08T06:45:06Z")

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Hello, I was trying to look at my scvi model using view\_anndata\_setup, but got the error below that says ‘rich has no attribute pretty’. I was actually able to do everything else, like train my model completely fine. Eve…

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## [Getting normalized expression](https://discourse.scverse.org/t/getting-normalized-expression/3976)

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**Author:** [@Kray](https://discourse.scverse.org/u/Kray)\
**Replies:** 13\
**Last updated:** [May 13, 2026, 9:54am UTC](https://discourse.scverse.org/t/getting-normalized-expression/3976 "2026-05-13T09:54:49Z")

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Hi, I am working on a big sized scRNAseq atlas with 2 million cells. I want to get the normalized expression. However, since it returns a data frame/numpy array, I run out of memory every time I am trying to retrieve th…

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## [Mapping 10X Xenium 5k data to scRNA-seq reference](https://discourse.scverse.org/t/mapping-10x-xenium-5k-data-to-scrna-seq-reference/3953)

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**Author:** [@Furbelox](https://discourse.scverse.org/u/Furbelox)\
**Replies:** 3\
**Last updated:** [April 23, 2026, 9:26am UTC](https://discourse.scverse.org/t/mapping-10x-xenium-5k-data-to-scrna-seq-reference/3953 "2026-04-23T09:26:33Z")

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Hello everyone, I’m desperately trying to create a latent space from my scRNA-seq reference and map my Xenium cells to that. “Reference mapping with scvi-tools” worked well for each dataset individually, but together, r…

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## [MRVI Jax Error "Invalid component distribution"](https://discourse.scverse.org/t/mrvi-jax-error-invalid-component-distribution/3959)

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**Author:** [@ggruenhagen3](https://discourse.scverse.org/u/ggruenhagen3)\
**Replies:** 3\
**Last updated:** [April 13, 2026, 2:27pm UTC](https://discourse.scverse.org/t/mrvi-jax-error-invalid-component-distribution/3959 "2026-04-13T14:27:55Z")

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Hello! I am trying to run MRVI on some scRNAseq data and ran into an error (listed below) during model.train(). I initially ran into this error when using jax version 0.9.2 and I saw in the first line of output from mode…

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## [Plotting the tangram imputed spatial data with spatialdata\_plot](https://discourse.scverse.org/t/plotting-the-tangram-imputed-spatial-data-with-spatialdata-plot/3942)

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**Author:** [@mdka00001](https://discourse.scverse.org/u/mdka00001)\
**Replies:** 3\
**Last updated:** [March 11, 2026, 2:02pm UTC](https://discourse.scverse.org/t/plotting-the-tangram-imputed-spatial-data-with-spatialdata-plot/3942 "2026-03-11T14:02:10Z")

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I am trying to plot the features of my tangram imupted spatial data by using the spatial image and cell segmentation of my reference spatial data. In general, I want to render a plot as below: However, only replacing…

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## [Pseudobulk after Performing integration with scatlasvae or scVI?](https://discourse.scverse.org/t/pseudobulk-after-performing-integration-with-scatlasvae-or-scvi/3821)

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**Author:** [@Indianhedgehog](https://discourse.scverse.org/u/Indianhedgehog)\
**Replies:** 4\
**Last updated:** [January 23, 2026, 5:37am UTC](https://discourse.scverse.org/t/pseudobulk-after-performing-integration-with-scatlasvae-or-scvi/3821 "2026-01-23T05:37:19Z")

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Hey everyone, I have integrated my dataset with CD8 dataset Integrative mapping of human CD8+ T cells in inflammation and cancer | Nature Methods, and it integration looks good. I was interested in performing pseudobulk…

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## [Predict cell type with scANVI for spatial transcriptomics data (Xenium)](https://discourse.scverse.org/t/predict-cell-type-with-scanvi-for-spatial-transcriptomics-data-xenium/3867)

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**Author:** [@spatts14](https://discourse.scverse.org/u/spatts14)\
**Replies:** 7\
**Last updated:** [December 28, 2025, 2:31pm UTC](https://discourse.scverse.org/t/predict-cell-type-with-scanvi-for-spatial-transcriptomics-data-xenium/3867 "2025-12-28T14:31:08Z")

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Hi, Thanks so much for the amazing tools! I was hoping someone could help me. I have an in-house dataset of Xenium 5k data and I would like to predict the cell types using a reference dataset. As such, I am also tryin…

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## [Question about complex experiment](https://discourse.scverse.org/t/question-about-complex-experiment/3864)

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**Author:** [@dackjames](https://discourse.scverse.org/u/dackjames)\
**Replies:** 1\
**Last updated:** [November 25, 2025, 7:39pm UTC](https://discourse.scverse.org/t/question-about-complex-experiment/3864 "2025-11-25T19:39:01Z")

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Hi everyone, I’m starting a fairly complex experiment that includes 10x single-cell, single-nucleus, and 10x multiome (snRNA-seq + scATAC-seq from the same nucleus), with control and treatment groups spread across all t…

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## [Excluding Ig and ribosomal genes from HVG selection in scVI, best practice?](https://discourse.scverse.org/t/excluding-ig-and-ribosomal-genes-from-hvg-selection-in-scvi-best-practice/3833)

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**Author:** [@marencc](https://discourse.scverse.org/u/marencc)\
**Replies:** 1\
**Last updated:** [October 22, 2025, 9:15am UTC](https://discourse.scverse.org/t/excluding-ig-and-ribosomal-genes-from-hvg-selection-in-scvi-best-practice/3833 "2025-10-22T09:15:23Z")

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Hi everyone, I’m working with single-cell RNA-seq data from CD45⁺ immune cells (mostly lymphoid lineages) and integrating multiple batches using scVI, which so far has given the best batch correction results. We’re now…

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## [How to use scib benchmark-metrics evaluate the adata after BBKNN integretion](https://discourse.scverse.org/t/how-to-use-scib-benchmark-metrics-evaluate-the-adata-after-bbknn-integretion/3807)

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**Author:** [@wangflmi](https://discourse.scverse.org/u/wangflmi)\
**Replies:** 3\
**Last updated:** [October 7, 2025, 6:40am UTC](https://discourse.scverse.org/t/how-to-use-scib-benchmark-metrics-evaluate-the-adata-after-bbknn-integretion/3807 "2025-10-07T06:40:49Z")

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The paper showed we can use benchmark metrics to evaluate the adata after BBKNN integration. But I can only use some default functions in the benchmark-metrics package to get the batch-remove grades. For bio-conservation…

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## [Anchor-based integration methods](https://discourse.scverse.org/t/anchor-based-integration-methods/3743)

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**Author:** [@diop89890](https://discourse.scverse.org/u/diop89890)\
**Replies:** 1\
**Last updated:** [September 25, 2025, 12:49pm UTC](https://discourse.scverse.org/t/anchor-based-integration-methods/3743 "2025-09-25T12:49:40Z")

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Hi. I am working with flow cytometry data. I have two batches of PBMC samples with the exact same panel, 25 proteins. I have a ML model for cell type prediction on one batch (=anchor) and trying to apply it to another …

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## [How to Correct for Intra-Organ Batch Effects Without Removing Inter-Organ Differences?](https://discourse.scverse.org/t/how-to-correct-for-intra-organ-batch-effects-without-removing-inter-organ-differences/3731)

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**Author:** [@dacon06](https://discourse.scverse.org/u/dacon06)\
**Replies:** 6\
**Last updated:** [August 5, 2025, 11:11am UTC](https://discourse.scverse.org/t/how-to-correct-for-intra-organ-batch-effects-without-removing-inter-organ-differences/3731 "2025-08-05T11:11:34Z")

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Dear Community, I’m currently working on integrating a single-cell RNA-seq dataset of human mesenchymal stem cells (MSCs) using scvi-tools. The dataset includes 11 samples, each from a different donor, across four tissu…

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## [Can we use resolVI and squidpy to annotate a CosMX object based on a single cell reference?](https://discourse.scverse.org/t/can-we-use-resolvi-and-squidpy-to-annotate-a-cosmx-object-based-on-a-single-cell-reference/3747)

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**Author:** [@coarfa](https://discourse.scverse.org/u/coarfa)\
**Replies:** 1\
**Last updated:** [August 3, 2025, 6:14pm UTC](https://discourse.scverse.org/t/can-we-use-resolvi-and-squidpy-to-annotate-a-cosmx-object-based-on-a-single-cell-reference/3747 "2025-08-03T18:14:37Z")

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Hi, Are there tutorials or protocols to assign cell types in CosMX loaded via Squidpy based on a single cell reference ? I think ResolVI might help, but I did not found a clear end to end tutorial When annotating C…

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## [How to handle batch effects within the query dataset when using scArches + SCVI?](https://discourse.scverse.org/t/how-to-handle-batch-effects-within-the-query-dataset-when-using-scarches-scvi/3728)

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**Author:** [@ashenflower](https://discourse.scverse.org/u/ashenflower)\
**Replies:** 1\
**Last updated:** [July 31, 2025, 12:14pm UTC](https://discourse.scverse.org/t/how-to-handle-batch-effects-within-the-query-dataset-when-using-scarches-scvi/3728 "2025-07-31T12:14:23Z")

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Hello everyone, I’m new to scArches and currently exploring how it works in combination with SCVI, particularly for integrating new datasets into a reference atlas. I’m following this tutorial, where a SCVI model is fi…

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## [Shared cell types not mixing when integrating datasets from different species](https://discourse.scverse.org/t/shared-cell-types-not-mixing-when-integrating-datasets-from-different-species/3685)

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**Author:** [@sandcell10](https://discourse.scverse.org/u/sandcell10)\
**Replies:** 4\
**Last updated:** [June 19, 2025, 7:02pm UTC](https://discourse.scverse.org/t/shared-cell-types-not-mixing-when-integrating-datasets-from-different-species/3685 "2025-06-19T19:02:10Z")

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Hello, I am attempting to integrate datasets of the same tissue from different species. Some of the datasets are single-cell while some are single-nucleus. I thought that SCVI would work well for this task, however, as …

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## [SMART-seq and MARS-seq pipelines](https://discourse.scverse.org/t/smart-seq-and-mars-seq-pipelines/3681)

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**Author:** [@Roy](https://discourse.scverse.org/u/Roy)\
**Replies:** 1\
**Last updated:** [June 19, 2025, 5:56pm UTC](https://discourse.scverse.org/t/smart-seq-and-mars-seq-pipelines/3681 "2025-06-19T17:56:00Z")

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Hi all, I’ve been working on a Python-based single-cell pipeline for cross-study integration built around the scverse ecosystem. So far, it works well for 10x Genomics data, but I’m now looking to expand support to othe…

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## [Domain adaptation to pre-train batch correction model using paired data](https://discourse.scverse.org/t/domain-adaptation-to-pre-train-batch-correction-model-using-paired-data/3633)

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**Author:** [@Valerie](https://discourse.scverse.org/u/Valerie)\
**Replies:** 12\
**Last updated:** [May 27, 2025, 6:44am UTC](https://discourse.scverse.org/t/domain-adaptation-to-pre-train-batch-correction-model-using-paired-data/3633 "2025-05-27T06:44:23Z")

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Good afternoon scvi team! I am very new to the scvi tool and moslty have been working with scRNA-seq data within R environment. I came around a specific issue which scvi could potentially be well suited for so I would l…

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## [scVI batch correction clusters all cells from sample in a circle (potential artifact)](https://discourse.scverse.org/t/scvi-batch-correction-clusters-all-cells-from-sample-in-a-circle-potential-artifact/3664)

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**Author:** [@CocoConstant](https://discourse.scverse.org/u/CocoConstant)\
**Replies:** 14\
**Last updated:** [June 3, 2025, 9:05am UTC](https://discourse.scverse.org/t/scvi-batch-correction-clusters-all-cells-from-sample-in-a-circle-potential-artifact/3664 "2025-06-03T09:05:55Z")

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When using scVI for batch correction and clustering on my single-cell data, I observed an unusual result: all cells from the same sample are clustered in a circle, separated from the rest. Changes to n\_latent , training …

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## [How should I calculate the knn entropy using the leiden clusters?](https://discourse.scverse.org/t/how-should-i-calculate-the-knn-entropy-using-the-leiden-clusters/3537)

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**Author:** [@danli349](https://discourse.scverse.org/u/danli349)\
**Replies:** 1\
**Last updated:** [April 10, 2025, 7:55am UTC](https://discourse.scverse.org/t/how-should-i-calculate-the-knn-entropy-using-the-leiden-clusters/3537 "2025-04-10T07:55:39Z")

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Hello: How should I calculate the knn entropy using the leiden clusters? https://arxiv.org/pdf/1506.06501v1 Thanks a lot

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## [Understanding scVI integration inside R with Seurat v5 & SCTransform](https://discourse.scverse.org/t/understanding-scvi-integration-inside-r-with-seurat-v5-sctransform/3588)

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**Author:** [@y.grabovska](https://discourse.scverse.org/u/y.grabovska)\
**Replies:** 1\
**Last updated:** [April 6, 2025, 8:52am UTC](https://discourse.scverse.org/t/understanding-scvi-integration-inside-r-with-seurat-v5-sctransform/3588 "2025-04-06T08:52:48Z")

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I have a set of single-cell libraries from an drug treatment experiment - early timepoint, treatment/DMSO at 3 timepoints (21 libraries total). I have preprocessed each library separately with Seurat using SCTransform v…

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## [How to fix number of nodes used in HPC environment with scvi.train (via R & reticulate)?](https://discourse.scverse.org/t/how-to-fix-number-of-nodes-used-in-hpc-environment-with-scvi-train-via-r-reticulate/3579)

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**Author:** [@ZheFrench](https://discourse.scverse.org/u/ZheFrench)\
**Replies:** 8\
**Last updated:** [April 10, 2025, 6:01am UTC](https://discourse.scverse.org/t/how-to-fix-number-of-nodes-used-in-hpc-environment-with-scvi-train-via-r-reticulate/3579 "2025-04-10T06:01:55Z")

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Hi, I’m using scvi via R using reticulate. All cpu nodes of the clusters are used, I would like to restrain this behavior when I call model$train function. Also I wanted to know if I should start the integration from …

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## [inferCNVpy after running scVI with batch as key](https://discourse.scverse.org/t/infercnvpy-after-running-scvi-with-batch-as-key/848)

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**Author:** [@zvittorio](https://discourse.scverse.org/u/zvittorio)\
**Replies:** 5\
**Last updated:** [March 24, 2025, 7:19am UTC](https://discourse.scverse.org/t/infercnvpy-after-running-scvi-with-batch-as-key/848 "2025-03-24T07:19:32Z")

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Hi scverse community, I have at my disposal a bunch of datasets, of which one is a cancer patient while the other ones are the same organ but in a healthy condition. The idea is to use the cell types of the healthy sam…

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## [Error when running scvi.data.add\_dna\_sequence](https://discourse.scverse.org/t/error-when-running-scvi-data-add-dna-sequence/3549)

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**Author:** [@afarha5](https://discourse.scverse.org/u/afarha5)\
**Replies:** 1\
**Last updated:** [March 18, 2025, 8:08am UTC](https://discourse.scverse.org/t/error-when-running-scvi-data-add-dna-sequence/3549 "2025-03-18T08:08:00Z")

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Hello, I am getting an error when running simple commands like: import genomepy # Define genome directory genome\_dir = "data" # Install mm10 genomepy.install\_genome("mm10",provider="ensembl", genomes\_dir=genome\_dir) …

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## [SysVI model and normalized expression](https://discourse.scverse.org/t/sysvi-model-and-normalized-expression/3543)

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**Author:** [@danieljrichard](https://discourse.scverse.org/u/danieljrichard)\
**Replies:** 1\
**Last updated:** [March 15, 2025, 7:32am UTC](https://discourse.scverse.org/t/sysvi-model-and-normalized-expression/3543 "2025-03-15T07:32:36Z")

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Hello, I was working through this example for running SysVI: And tried running get\_normalized expression. However, I get this error: AttributeError: ‘SysVI’ object has no attribute ‘get\_normalized\_expression’ Howeve…

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## [Scvi-tools and xenium](https://discourse.scverse.org/t/scvi-tools-and-xenium/2450)

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**Author:** [@wangjiawen2013](https://discourse.scverse.org/u/wangjiawen2013)\
**Replies:** 7\
**Last updated:** [March 13, 2025, 5:58pm UTC](https://discourse.scverse.org/t/scvi-tools-and-xenium/2450 "2025-03-13T17:58:30Z")

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Hi, Can I use scvi-tools to process 10x genomics xenium spatial transcriptome dataset ? The following adata is an anndata object from xenium dataset. # Registering the data scvi.model.SCVI.setup\_anndata(adata, layer="c…

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## [Parameters in training model for integrating datasets with scVI in R](https://discourse.scverse.org/t/parameters-in-training-model-for-integrating-datasets-with-scvi-in-r/3522)

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**Author:** [@joweihsieh](https://discourse.scverse.org/u/joweihsieh)\
**Replies:** 13\
**Last updated:** [March 9, 2025, 12:36pm UTC](https://discourse.scverse.org/t/parameters-in-training-model-for-integrating-datasets-with-scvi-in-r/3522 "2025-03-09T12:36:23Z")

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Thanks for developing this tool!! I was trying to use scVI to integrate my datasets. Following the instructions (Integrating datasets with scVI in R — scvi-tools), I was able to run the script successfully without chang…

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## [TotalVI not fully integrating CITEseq cells with GEX and missing protein values](https://discourse.scverse.org/t/totalvi-not-fully-integrating-citeseq-cells-with-gex-and-missing-protein-values/3473)

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**Author:** [@timslittle](https://discourse.scverse.org/u/timslittle)\
**Replies:** 1\
**Last updated:** [February 6, 2025, 4:38pm UTC](https://discourse.scverse.org/t/totalvi-not-fully-integrating-citeseq-cells-with-gex-and-missing-protein-values/3473 "2025-02-06T16:38:49Z")

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Hi Team, Apologies if I’m doing something wrong here! I have a CITEseq dataset in which some cells have good quality RNAseq values but poor quality ADT, so these ADT values have been removed. I tried using TotalVI to i…

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