# Help

**URL:** https://discourse.scverse.org/c/help/27.md?page=2

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

**Page:** 3

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## [Imputation/Denoise output](https://discourse.scverse.org/t/imputation-denoise-output/3913)

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**Author:** [@Huiyueli](https://discourse.scverse.org/u/Huiyueli)\
**Replies:** 1\
**Last updated:** [January 15, 2026, 7:22am UTC](https://discourse.scverse.org/t/imputation-denoise-output/3913 "2026-01-15T07:22:32Z")

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When using the code below for data denoise/imputation, how to set the library\_size in get\_normalized\_expression()? to obtain the output in count-scale, rather than normalized output? scvi.model.SCVI.setup\_anndata(adata,…

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## [SCANVI Model Loading Issue: Partial Data and Workaround](https://discourse.scverse.org/t/scanvi-model-loading-issue-partial-data-and-workaround/3910)

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**Author:** [@Duvnii](https://discourse.scverse.org/u/Duvnii)\
**Replies:** 1\
**Last updated:** [January 11, 2026, 12:32pm UTC](https://discourse.scverse.org/t/scanvi-model-loading-issue-partial-data-and-workaround/3910 "2026-01-11T12:32:23Z")

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SCANVI Model Loading Issue: Partial Data and Workaround Hello, I’m experiencing an issue when trying to load a pre-trained SCANVI model with partial/incomplete data. The data I used is fully labeled. The model is traine…

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## [Error in training resolvi model](https://discourse.scverse.org/t/error-in-training-resolvi-model/3904)

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**Author:** [@zimmerma](https://discourse.scverse.org/u/zimmerma)\
**Replies:** 5\
**Last updated:** [January 5, 2026, 9:10pm UTC](https://discourse.scverse.org/t/error-in-training-resolvi-model/3904 "2026-01-05T21:10:39Z")

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Hello, I am running the tutorial for ResolVI. However when I get to the line of code supervised\_resolvi.train(max\_epochs=50)I get the following error. Exception raised during training. \<class ‘NameError’\> Input argume…

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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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## [Remove ribosomal genes driving variation (on PC plot)?](https://discourse.scverse.org/t/remove-ribosomal-genes-driving-variation-on-pc-plot/3902)

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**Author:** [@npont](https://discourse.scverse.org/u/npont)\
**Replies:** 0\
**Last updated:** [December 17, 2025, 10:19am UTC](https://discourse.scverse.org/t/remove-ribosomal-genes-driving-variation-on-pc-plot/3902 "2025-12-17T10:19:59Z")

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Hi all, Following the tutorial of scanpy about clustering ( Preprocessing and clustering — scanpy ), I plotted some QC metrics (computed with sc.pp.calculate\_qc\_metrics(adata, qc\_vars=\[“mt”, “ribo”\])) on the first four …

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## [Sc.pp.filter\_genes how to use](https://discourse.scverse.org/t/sc-pp-filter-genes-how-to-use/3901)

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**Author:** [@baicai](https://discourse.scverse.org/u/baicai)\
**Replies:** 0\
**Last updated:** [December 16, 2025, 6:41am UTC](https://discourse.scverse.org/t/sc-pp-filter-genes-how-to-use/3901 "2025-12-16T06:41:06Z")

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I would like to ask for clarification regarding the recommended order of sc.pp.filter\_genes and sc.pp.normalize\_total, and the intended interpretation of their interaction. It is clear that filtering genes (e.g. min\_c…

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## [What is the context or history of having both inplace and copy args everywhere?](https://discourse.scverse.org/t/what-is-the-context-or-history-of-having-both-inplace-and-copy-args-everywhere/3900)

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**Author:** [@patcon](https://discourse.scverse.org/u/patcon)\
**Replies:** 1\
**Last updated:** [December 15, 2025, 9:49pm UTC](https://discourse.scverse.org/t/what-is-the-context-or-history-of-having-both-inplace-and-copy-args-everywhere/3900 "2025-12-15T21:49:42Z")

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First off, thanks for this wonderful tool! I left open science back in 2008, took a round-about tour into tech, and am now coming back. I’m feeling very energized while exploring it :slight\_smile: I’m trying to extend s…

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## [Questions on Shapes + Tables vs single AnnData object](https://discourse.scverse.org/t/questions-on-shapes-tables-vs-single-anndata-object/3814)

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**Author:** [@LucaMarconato](https://discourse.scverse.org/u/LucaMarconato)\
**Replies:** 6\
**Last updated:** [December 11, 2025, 10:02pm UTC](https://discourse.scverse.org/t/questions-on-shapes-tables-vs-single-anndata-object/3814 "2025-12-11T22:02:03Z")

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Moving the conversation from a GitHub issue to here. Original message from asmlgkj (curry\_fan) · GitHub I have a couple of questions regarding the SpatialData outputs and how cell positions are represented in Seurat o…

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## [Issue with scVI VAE reconstruction: High sensitivity to library size and poor rank preservation](https://discourse.scverse.org/t/issue-with-scvi-vae-reconstruction-high-sensitivity-to-library-size-and-poor-rank-preservation/3883)

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**Author:** [@hamidsta](https://discourse.scverse.org/u/hamidsta)\
**Replies:** 1\
**Last updated:** [December 9, 2025, 2:58pm UTC](https://discourse.scverse.org/t/issue-with-scvi-vae-reconstruction-high-sensitivity-to-library-size-and-poor-rank-preservation/3883 "2025-12-09T14:58:30Z")

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Hello :smiley: , I am running scVI VAE tool, with the goal of analyzing both the learned cell embeddings and the reconstructed gene expression. ( i have merfish sample ) I want to verify if the gene ranking is preser…

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## [Issue with multiVI get\_normalized\_expression and get\_normalized\_accessibility](https://discourse.scverse.org/t/issue-with-multivi-get-normalized-expression-and-get-normalized-accessibility/3878)

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**Author:** [@andywangzhou](https://discourse.scverse.org/u/andywangzhou)\
**Replies:** 5\
**Last updated:** [December 7, 2025, 7:22am UTC](https://discourse.scverse.org/t/issue-with-multivi-get-normalized-expression-and-get-normalized-accessibility/3878 "2025-12-07T07:22:37Z")

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Hi developers and the community, I’m getting this issue running the MultiVI as instructed in the tutorial: imputed\_expression = model.get\_normalized\_expression() \>\>\> imputed\_expression …

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## [Scvi 1.4.0. model.differential\_expression outputs](https://discourse.scverse.org/t/scvi-1-4-0-model-differential-expression-outputs/3893)

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**Author:** [@cagla](https://discourse.scverse.org/u/cagla)\
**Replies:** 1\
**Last updated:** [December 7, 2025, 7:21am UTC](https://discourse.scverse.org/t/scvi-1-4-0-model-differential-expression-outputs/3893 "2025-12-07T07:21:00Z")

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Hello, I am using the scvi version 1.4.0.post1. The model.differential\_expression function gives proba\_m1, proba\_m2, bayes\_factor, scale1, scale2, raw\_mean1, raw\_mean2, non\_zeros\_proportion1, non\_zeros\_proportion2, raw\_n…

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## [CellFlow as a training framework vs pretrained model](https://discourse.scverse.org/t/cellflow-as-a-training-framework-vs-pretrained-model/3879)

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**Author:** [@tnnandi](https://discourse.scverse.org/u/tnnandi)\
**Replies:** 1\
**Last updated:** [December 5, 2025, 3:17pm UTC](https://discourse.scverse.org/t/cellflow-as-a-training-framework-vs-pretrained-model/3879 "2025-12-05T15:17:31Z")

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I’m looking for a pretrained model that I can use to generate the perturbed cell state in response to genetic/chemical perturbations, and I came across CellFlow. I just wanted to confirm whether CellFlow is i) a trainin…

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## [Draw\_graph results in a cloud or nice PAGA-like structure depending on dataset?](https://discourse.scverse.org/t/draw-graph-results-in-a-cloud-or-nice-paga-like-structure-depending-on-dataset/3891)

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**Author:** [@Miglio](https://discourse.scverse.org/u/Miglio)\
**Replies:** 0\
**Last updated:** [December 4, 2025, 6:10pm UTC](https://discourse.scverse.org/t/draw-graph-results-in-a-cloud-or-nice-paga-like-structure-depending-on-dataset/3891 "2025-12-04T18:10:41Z")

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Hello, I turned to scanpy to analyze metacells datasets and I am intrigued by the draw\_graph to show data toppology, potentially with PAGA or MST. For one of my datasets it worked beautifully with the metacell clusters …

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## [Limited cell types in reference dataset for scANVI](https://discourse.scverse.org/t/limited-cell-types-in-reference-dataset-for-scanvi/3886)

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**Author:** [@ayyldz](https://discourse.scverse.org/u/ayyldz)\
**Replies:** 3\
**Last updated:** [December 4, 2025, 1:40pm UTC](https://discourse.scverse.org/t/limited-cell-types-in-reference-dataset-for-scanvi/3886 "2025-12-04T13:40:10Z")

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Thank you for developing such powerful tools, very useful! I am trying to annotate some immature cell type populations in adult dataset and I am using fetal sample dataset as reference where these immature population is…

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## [Seeking guidance and reviewers for AnnData HTML representation PR (#2236)](https://discourse.scverse.org/t/seeking-guidance-and-reviewers-for-anndata-html-representation-pr-2236/3884)

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**Author:** [@katosh](https://discourse.scverse.org/u/katosh)\
**Replies:** 2\
**Last updated:** [December 1, 2025, 11:21pm UTC](https://discourse.scverse.org/t/seeking-guidance-and-reviewers-for-anndata-html-representation-pr-2236/3884 "2025-12-01T23:21:20Z")

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Hi all, I just opened a PR to AnnData that adds a full HTML representation for AnnData objects ( Add HTML representation by katosh · Pull Request #2236 · scverse/anndata · GitHub ). It’s a fairly extensive implementatio…

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## [Corrected count for resolvi](https://discourse.scverse.org/t/corrected-count-for-resolvi/3870)

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**Author:** [@ynanli](https://discourse.scverse.org/u/ynanli)\
**Replies:** 1\
**Last updated:** [November 25, 2025, 7:42pm UTC](https://discourse.scverse.org/t/corrected-count-for-resolvi/3870 "2025-11-25T19:42:09Z")

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Hi, I am wondering what would be the right way of generating a corrected count matrix for downstream analysis from resolvi. The tutorial uses the median of px\_rate as generated\_expression, while the preprint computed c…

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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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## [Loss\_z1\_weight and loss\_z1\_unweight in scANVI](https://discourse.scverse.org/t/loss-z1-weight-and-loss-z1-unweight-in-scanvi/364)

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**Author:** [@yugeji](https://discourse.scverse.org/u/yugeji)\
**Replies:** 3\
**Last updated:** [November 25, 2025, 7:32pm UTC](https://discourse.scverse.org/t/loss-z1-weight-and-loss-z1-unweight-in-scanvi/364 "2025-11-25T19:32:13Z")

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In the scANVI implementation, there are two losses I don’t quite understand: scvi-tools/\_scanvae.py at d636093bc8d49c8e03fcb4bc0a8bc8130cb29fe2 · scverse/scvi-tools · GitHub loss\_z1\_unweight = -Normal(pz1\_m, torch.sqrt(…

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## [Inquiry Regarding DRVI Model Compatibility with scANVI for Embedding Optimization?](https://discourse.scverse.org/t/inquiry-regarding-drvi-model-compatibility-with-scanvi-for-embedding-optimization/3876)

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**Author:** [@Xicici-Yan](https://discourse.scverse.org/u/Xicici-Yan)\
**Replies:** 1\
**Last updated:** [November 25, 2025, 7:21pm UTC](https://discourse.scverse.org/t/inquiry-regarding-drvi-model-compatibility-with-scanvi-for-embedding-optimization/3876 "2025-11-25T19:21:12Z")

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I am writing to inquire about the compatibility of the DRVI model with scANVI for embedding optimization. Specifically, I would like to know: Whether the DRVI model supports using scANVI to optimize embeddings, and if…

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## [Spatialdata.aggregate, image and segmentation\_mask have different shape, but aligned in 'global'](https://discourse.scverse.org/t/spatialdata-aggregate-image-and-segmentation-mask-have-different-shape-but-aligned-in-global/3650)

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**Author:** [@kare9758](https://discourse.scverse.org/u/kare9758)\
**Replies:** 4\
**Last updated:** [November 21, 2025, 6:46pm UTC](https://discourse.scverse.org/t/spatialdata-aggregate-image-and-segmentation-mask-have-different-shape-but-aligned-in-global/3650 "2025-11-21T18:46:50Z")

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Thanks for the great package! I have an image and a cell mask, I want to quantify the mean intensity of the signal measured in the image within each cell, using the cell mask. The image is a lot smaller, with size (3,91…

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## [.raw. car\_names reassignation](https://discourse.scverse.org/t/raw-car-names-reassignation/3872)

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**Author:** [@bontix-77](https://discourse.scverse.org/u/bontix-77)\
**Replies:** 2\
**Last updated:** [November 20, 2025, 4:34pm UTC](https://discourse.scverse.org/t/raw-car-names-reassignation/3872 "2025-11-20T16:34:24Z")

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After SeuratDisk the raw.var\_names contain the numeric index while raw.var\[‘\_index’\] contain the gene symbols. I need to swap the two but raw data are no mutable, is all locked. Suggestions?

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## [Sc.tl.ingest over representing rare cell types in spatial transcriptomics data](https://discourse.scverse.org/t/sc-tl-ingest-over-representing-rare-cell-types-in-spatial-transcriptomics-data/3868)

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**Author:** [@spatts14](https://discourse.scverse.org/u/spatts14)\
**Replies:** 0\
**Last updated:** [November 18, 2025, 8:46am UTC](https://discourse.scverse.org/t/sc-tl-ingest-over-representing-rare-cell-types-in-spatial-transcriptomics-data/3868 "2025-11-18T08:46:43Z")

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I am trying to use sc.tl.ingest to predict cell types for my Xenium 5k spatial transcriptomics data. I have subsetted the reference dataset to only contain the disease types and tissue types that are present in my STx d…

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## [Training not using the full GPU](https://discourse.scverse.org/t/training-not-using-the-full-gpu/3857)

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**Author:** [@mys\_721tx](https://discourse.scverse.org/u/mys_721tx)\
**Replies:** 3\
**Last updated:** [November 10, 2025, 2:35pm UTC](https://discourse.scverse.org/t/training-not-using-the-full-gpu/3857 "2025-11-10T14:35:50Z")

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So I have been running training couple models recently and I encountered this one problem. scvi has no problem detecting CUDA or the GPU. But the problem is that it is using about 25% of GPU and 20% of VRAMs. Have any of…

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## [Impact of scaling on clustering results and controlling minimum cluster size in Leiden clustering](https://discourse.scverse.org/t/impact-of-scaling-on-clustering-results-and-controlling-minimum-cluster-size-in-leiden-clustering/3849)

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**Author:** [@asmlgkj](https://discourse.scverse.org/u/asmlgkj)\
**Replies:** 1\
**Last updated:** [November 10, 2025, 9:19am UTC](https://discourse.scverse.org/t/impact-of-scaling-on-clustering-results-and-controlling-minimum-cluster-size-in-leiden-clustering/3849 "2025-11-10T09:19:14Z")

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Description Hi scanpy team, I’ve encountered two related issues with clustering that I’d like to understand better: Issue 1: Dramatic difference in cluster numbers with/without scaling I’m observing a significant dis…

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## [How should I process the data after removing low-quality cell clusters?](https://discourse.scverse.org/t/how-should-i-process-the-data-after-removing-low-quality-cell-clusters/3855)

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**Author:** [@XJY](https://discourse.scverse.org/u/XJY)\
**Replies:** 0\
**Last updated:** [November 9, 2025, 7:00pm UTC](https://discourse.scverse.org/t/how-should-i-process-the-data-after-removing-low-quality-cell-clusters/3855 "2025-11-09T19:00:40Z")

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I have already completed the standard single-cell analysis workflow, but I found that one cluster consisted of low-quality cells. I want to remove this cluster, and an AI suggested that I should rerun the preprocessing …

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## [How to use totalVI denoised protein measurements](https://discourse.scverse.org/t/how-to-use-totalvi-denoised-protein-measurements/3850)

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**Author:** [@Zoe](https://discourse.scverse.org/u/Zoe)\
**Replies:** 1\
**Last updated:** [November 9, 2025, 12:58pm UTC](https://discourse.scverse.org/t/how-to-use-totalvi-denoised-protein-measurements/3850 "2025-11-09T12:58:56Z")

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Hi! I have a sort of theoretical question about the totalVI denoised protein measurements. From the paper, it seems like for the RNA modality, there is a specific library size-based scaling factor, but it doesn’t seem li…

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## [Rank\_genes\_groups expects log data but default to adata.raw, why?](https://discourse.scverse.org/t/rank-genes-groups-expects-log-data-but-default-to-adata-raw-why/3852)

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**Author:** [@luguna](https://discourse.scverse.org/u/luguna)\
**Replies:** 0\
**Last updated:** [November 7, 2025, 5:19pm UTC](https://discourse.scverse.org/t/rank-genes-groups-expects-log-data-but-default-to-adata-raw-why/3852 "2025-11-07T17:19:40Z")

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Hi all, I am relatively new to single-cell (and spatial) data analysis. I was following this pipeline to try to replicate an analysis, and it had the following steps: sc.pp.filter\_cells(adata,min\_counts=40) sc.pp.filte…

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## [Convert Scanpy (h5ad) to Seurat (rds)](https://discourse.scverse.org/t/convert-scanpy-h5ad-to-seurat-rds/457)

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**Author:** [@PEB](https://discourse.scverse.org/u/PEB)\
**Replies:** 10\
**Last updated:** [November 6, 2025, 11:14am UTC](https://discourse.scverse.org/t/convert-scanpy-h5ad-to-seurat-rds/457 "2025-11-06T11:14:51Z")

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Hi Everyone, I am trying to convert my h5ad to a Seurat rds to run R-based pseudo time algorithms (monocle, slingshot, etc). However I keep running into errors on the commonly posted methods. Does anyone have any advice…

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## [Question about get\_normalized\_expression computation](https://discourse.scverse.org/t/question-about-get-normalized-expression-computation/3842)

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**Author:** [@racng](https://discourse.scverse.org/u/racng)\
**Replies:** 3\
**Last updated:** [November 5, 2025, 8:14am UTC](https://discourse.scverse.org/t/question-about-get-normalized-expression-computation/3842 "2025-11-05T08:14:27Z")

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I have trained a TOTALVI model and I am using the get\_normalized\_expression function to get imputed values for one gene and one protein. It is using mostly CPUs (128 threads) and not the GPU (Volatile GPU-Util = 8%, 2391…

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## [Batch key and categorical variables for get\_normalized\_expression()](https://discourse.scverse.org/t/batch-key-and-categorical-variables-for-get-normalized-expression/3841)

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**Author:** [@munta](https://discourse.scverse.org/u/munta)\
**Replies:** 2\
**Last updated:** [November 4, 2025, 11:01am UTC](https://discourse.scverse.org/t/batch-key-and-categorical-variables-for-get-normalized-expression/3841 "2025-11-04T11:01:55Z")

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Hi. many thanks for the nice tool. I have combined multiple public scRNA-seq data and used scvi-tool for integration. scvi.model.SCVI.setup\_anndata(adata, layer="counts", batch\_key="Project", …

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