# Help

**URL:** https://discourse.scverse.org/c/help/27.md?page=3

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

**Page:** 4

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## [Same scVI model with different values on mac silicon and linux?!](https://discourse.scverse.org/t/same-scvi-model-with-different-values-on-mac-silicon-and-linux/3846)

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**Author:** [@munta](https://discourse.scverse.org/u/munta)\
**Replies:** 1\
**Last updated:** [November 4, 2025, 7:09am UTC](https://discourse.scverse.org/t/same-scvi-model-with-different-values-on-mac-silicon-and-linux/3846 "2025-11-04T07:09:02Z")

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Hi. I have used scvi model to integrate data from different batches. I used HPC cluster and gpu for that. when I checked the data on cluster adata.layers\['scvi\_norm'\] = vae.get\_normalized\_expression(adata=adata,librar…

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## [Question about implementation of highly\_variable\_genes](https://discourse.scverse.org/t/question-about-implementation-of-highly-variable-genes/3847)

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**Author:** [@ekgrantham](https://discourse.scverse.org/u/ekgrantham)\
**Replies:** 0\
**Last updated:** [November 3, 2025, 4:10pm UTC](https://discourse.scverse.org/t/question-about-implementation-of-highly-variable-genes/3847 "2025-11-03T16:10:36Z")

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When performing scanpy.pp.highly\_variable\_genes, documentation states that “Depending on flavor, this reproduces the R-implementations of Seurat…” does this mean it reproduces the latest version of Seurat? I am wondering…

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## [Calculate gene signature scores from cell2location-deconvolved spatial transcriptomics](https://discourse.scverse.org/t/calculate-gene-signature-scores-from-cell2location-deconvolved-spatial-transcriptomics/3836)

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**Author:** [@victorsanchezarevalo](https://discourse.scverse.org/u/victorsanchezarevalo)\
**Replies:** 0\
**Last updated:** [October 22, 2025, 1:11pm UTC](https://discourse.scverse.org/t/calculate-gene-signature-scores-from-cell2location-deconvolved-spatial-transcriptomics/3836 "2025-10-22T13:11:47Z")

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Hi everyone, I’m working with Visium spatial transcriptomics data and have performed deconvolution using cell2location. Now I want to calculate a gene signature score (e.g., an acidosis signature) and I’m unsure about t…

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## [Pathway quantification with decoupler - questions on the possible inputs](https://discourse.scverse.org/t/pathway-quantification-with-decoupler-questions-on-the-possible-inputs/3834)

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**Author:** [@merlevede](https://discourse.scverse.org/u/merlevede)\
**Replies:** 3\
**Last updated:** [October 22, 2025, 12:45pm UTC](https://discourse.scverse.org/t/pathway-quantification-with-decoupler-questions-on-the-possible-inputs/3834 "2025-10-22T12:45:43Z")

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Hello, This is my first post on the scverse forum - I could not find a way to tag decoupler here, but I hope my questions will still reach the right people! I have a few questions related to gene set quantification, pa…

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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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## [Potential bug in scvi.model.TOTALVI.setup\_mudata](https://discourse.scverse.org/t/potential-bug-in-scvi-model-totalvi-setup-mudata/3822)

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**Author:** [@igrisch](https://discourse.scverse.org/u/igrisch)\
**Replies:** 2\
**Last updated:** [October 10, 2025, 4:30pm UTC](https://discourse.scverse.org/t/potential-bug-in-scvi-model-totalvi-setup-mudata/3822 "2025-10-10T16:30:03Z")

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Hi there, I am using the most recent github version of scvi and have been running into this potential bug when I try to set up my data. It occurs when I use mudata or anndata. Basically, it looks like something is ha…

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## [Changing the order of the anndata objects in anndata.concat changes the leiden clustering](https://discourse.scverse.org/t/changing-the-order-of-the-anndata-objects-in-anndata-concat-changes-the-leiden-clustering/3802)

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**Author:** [@osmanmerdan](https://discourse.scverse.org/u/osmanmerdan)\
**Replies:** 6\
**Last updated:** [October 9, 2025, 7:45am UTC](https://discourse.scverse.org/t/changing-the-order-of-the-anndata-objects-in-anndata-concat-changes-the-leiden-clustering/3802 "2025-10-09T07:45:09Z")

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Hi everyone, When I change the order of anndata objects in anndata concat, like the following: adata1 = ad.concat(\[day1\_data, day2\_data, day3\_data\], join='outer') adata2 = ad.concat(\[day2\_data, day1\_data, day3\_data\], j…

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## [Infercnvpy | get positional information for bins](https://discourse.scverse.org/t/infercnvpy-get-positional-information-for-bins/3820)

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**Author:** [@Werner](https://discourse.scverse.org/u/Werner)\
**Replies:** 0\
**Last updated:** [October 7, 2025, 11:57am UTC](https://discourse.scverse.org/t/infercnvpy-get-positional-information-for-bins/3820 "2025-10-07T11:57:55Z")

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Hello everybody, I would like to know if it is possible to get the chromosomal start and stop positions of the windows generated by infercnvpy after running infercnvpy.tl.infercnv(). This would be very helpful as I wan…

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## [Help with package setup](https://discourse.scverse.org/t/help-with-package-setup/3811)

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**Author:** [@josenimo](https://discourse.scverse.org/u/josenimo)\
**Replies:** 2\
**Last updated:** [October 7, 2025, 10:46am UTC](https://discourse.scverse.org/t/help-with-package-setup/3811 "2025-10-07T10:46:39Z")

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Hey all, First, I am not sure this is the right place to post this. But I looked through this discourse and through Zulip, and I could not find a better place. I am a single developer working on the openDVP package, wh…

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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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## [Is Gaussian mixture VAE implemented in scVI-tools?](https://discourse.scverse.org/t/is-gaussian-mixture-vae-implemented-in-scvi-tools/3809)

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**Author:** [@mikeshen](https://discourse.scverse.org/u/mikeshen)\
**Replies:** 3\
**Last updated:** [September 25, 2025, 8:29pm UTC](https://discourse.scverse.org/t/is-gaussian-mixture-vae-implemented-in-scvi-tools/3809 "2025-09-25T20:29:56Z")

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Hi, Is Gaussian mixture VAE framework (GMVAE), one used in e.g. scVAE (scVAE: Single-cell variational auto-encoders — scVAE 2.1.4 documentation), also implemented in scVI-tools? Thanks!

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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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## [Posterior probability interpretability (soft=True)](https://discourse.scverse.org/t/posterior-probability-interpretability-soft-true/3787)

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**Author:** [@ondy](https://discourse.scverse.org/u/ondy)\
**Replies:** 1\
**Last updated:** [September 25, 2025, 12:46pm UTC](https://discourse.scverse.org/t/posterior-probability-interpretability-soft-true/3787 "2025-09-25T12:46:32Z")

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Hello, I used scANVI to transfer cell type labels from a single-cell reference to my spatial transcriptomics data (MERFISH). I assigned labels at three hierarchical levels and then compared the prediction scores obtain…

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## [Cell charter niche calling](https://discourse.scverse.org/t/cell-charter-niche-calling/2192)

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**Author:** [@abs51295](https://discourse.scverse.org/u/abs51295)\
**Replies:** 5\
**Last updated:** [September 13, 2025, 7:58am UTC](https://discourse.scverse.org/t/cell-charter-niche-calling/2192 "2025-09-13T07:58:43Z")

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Hey, Thank you for the cell charter tool! @marcovarrone. We find the tool really useful in getting niches. Reading the paper and running it on our internal Xenium data, we find that an extremely small group of cells wou…

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## [Preprocess of scATAC use for peakVI or MultiVII](https://discourse.scverse.org/t/preprocess-of-scatac-use-for-peakvi-or-multivii/3795)

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**Author:** [@dfgfdgfd1](https://discourse.scverse.org/u/dfgfdgfd1)\
**Replies:** 0\
**Last updated:** [September 12, 2025, 12:47pm UTC](https://discourse.scverse.org/t/preprocess-of-scatac-use-for-peakvi-or-multivii/3795 "2025-09-12T12:47:26Z")

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I processed scATAC data with snapatac2, but snapatac2 output scATAC in bin counts (not peak counts). I tired many tools to integrate scRNA and scATAC with bin couns (5k) or gene activity matrix generated from bin counts …

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## [Preprocess of scATAC use for peakVI or MultiVI](https://discourse.scverse.org/t/preprocess-of-scatac-use-for-peakvi-or-multivi/3691)

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**Author:** [@Xuann](https://discourse.scverse.org/u/Xuann)\
**Replies:** 5\
**Last updated:** [September 3, 2025, 9:39pm UTC](https://discourse.scverse.org/t/preprocess-of-scatac-use-for-peakvi-or-multivi/3691 "2025-09-03T21:39:39Z")

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Hi, Many thanks for providing scvi-tools, it do helps a lot when I integrate multiple datasets. I processed scATAC data with snapatac2, but snapatac2 output scATAC in bin counts (not peak counts). I tired many tools to…

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## [Memory Usage in multiple New Formats](https://discourse.scverse.org/t/memory-usage-in-multiple-new-formats/3605)

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**Author:** [@Mariano](https://discourse.scverse.org/u/Mariano)\
**Replies:** 2\
**Last updated:** [September 2, 2025, 10:20am UTC](https://discourse.scverse.org/t/memory-usage-in-multiple-new-formats/3605 "2025-09-02T10:20:21Z")

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Hi, there are now, multiple ways of loading an anndata object. I will list some: read\_h5ad, read\_h5ad(backed=‘r’), read\_zarr, read\_lazy (in the experimental branch). I am having a difficult time to understand the differ…

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## [How can I operate on view of Anndata object when the Object itself is large to load to memory?](https://discourse.scverse.org/t/how-can-i-operate-on-view-of-anndata-object-when-the-object-itself-is-large-to-load-to-memory/3788)

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**Author:** [@MooseGoblin89](https://discourse.scverse.org/u/MooseGoblin89)\
**Replies:** 1\
**Last updated:** [September 2, 2025, 10:14am UTC](https://discourse.scverse.org/t/how-can-i-operate-on-view-of-anndata-object-when-the-object-itself-is-large-to-load-to-memory/3788 "2025-09-02T10:14:07Z")

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Hi All, I am new to using AnnData, and seem to be struggling with some basic usage– I am using large (\>10GB) snRNA-seq files from Allen Brain in .h5ad format. I can only load these as backed Anndata objects (backed=’r’)…

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## [Error ir.tl.summarize\_clonal\_expansion](https://discourse.scverse.org/t/error-ir-tl-summarize-clonal-expansion/3789)

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**Author:** [@m21camby](https://discourse.scverse.org/u/m21camby)\
**Replies:** 2\
**Last updated:** [September 2, 2025, 9:25am UTC](https://discourse.scverse.org/t/error-ir-tl-summarize-clonal-expansion/3789 "2025-09-02T09:25:28Z")

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Hi, I’m having error while running summarize\_clonal\_expansion function. It works with old metrics (e.g. days) but gets errors with new metrics that I concatenate (e.g. annotation\_lvl2\_marker\_draining\_days). Thank you! …

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## [multiVI speed and cpu consumption](https://discourse.scverse.org/t/multivi-speed-and-cpu-consumption/3714)

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**Author:** [@bxxu](https://discourse.scverse.org/u/bxxu)\
**Replies:** 2\
**Last updated:** [August 30, 2025, 9:16pm UTC](https://discourse.scverse.org/t/multivi-speed-and-cpu-consumption/3714 "2025-08-30T21:16:19Z")

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Hi developers, I am using multiVI (from scvi-tools 1.3.2) to analyze the processed pbmc10k data following the tutorial. For some reason, training is really slow, it takes 15 seconds for 1 epoch. In addition, multiVI is c…

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## [Get\_normalized\_expression causes my kernel to disconnect](https://discourse.scverse.org/t/get-normalized-expression-causes-my-kernel-to-disconnect/3778)

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**Author:** [@eviezh](https://discourse.scverse.org/u/eviezh)\
**Replies:** 1\
**Last updated:** [August 19, 2025, 7:13am UTC](https://discourse.scverse.org/t/get-normalized-expression-causes-my-kernel-to-disconnect/3778 "2025-08-19T07:13:21Z")

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Hey everyone! fairly new user of scvi-tools and sCANVI here. Every time I run get\_normalized\_expression on my sCANVI query model, my kernel says it disconnects (which I believe is likely a memory issue?) This is actual…

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## [Decoupler error: raw input data has integers, will not accept "skip\_checks=True"](https://discourse.scverse.org/t/decoupler-error-raw-input-data-has-integers-will-not-accept-skip-checks-true/3779)

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**Author:** [@mmartimis](https://discourse.scverse.org/u/mmartimis)\
**Replies:** 1\
**Last updated:** [August 19, 2025, 11:30pm UTC](https://discourse.scverse.org/t/decoupler-error-raw-input-data-has-integers-will-not-accept-skip-checks-true/3779 "2025-08-19T23:30:37Z")

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Hi, I’m trying to run decoupler for a pesudobulk analysis of my data. However, when I’m trying to run the following code: pdata = dc.pp.pseudobulk(adata, sample\_col="sample", groups\_col="annotation", layer='rawcounts',…

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## [SpatialData workflow](https://discourse.scverse.org/t/spatialdata-workflow/3740)

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**Author:** [@revalescente](https://discourse.scverse.org/u/revalescente)\
**Replies:** 3\
**Last updated:** [August 12, 2025, 3:27pm UTC](https://discourse.scverse.org/t/spatialdata-workflow/3740 "2025-08-12T15:27:57Z")

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Hello, I’m a biostatistician working on a project with visiumHD data and I’d like to use spatialdata objects as the backbone of the segmentation process. I’m used to work with R and probably my supervisor will prefer th…

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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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## [Conduct SCANVI after running SysVI on multi-platform data](https://discourse.scverse.org/t/conduct-scanvi-after-running-sysvi-on-multi-platform-data/3745)

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**Author:** [@coarfa](https://discourse.scverse.org/u/coarfa)\
**Replies:** 3\
**Last updated:** [August 3, 2025, 4:34pm UTC](https://discourse.scverse.org/t/conduct-scanvi-after-running-sysvi-on-multi-platform-data/3745 "2025-08-03T16:34:52Z")

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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 w…

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## [How to filter out specific cell types in spatialdata similar to anndata?](https://discourse.scverse.org/t/how-to-filter-out-specific-cell-types-in-spatialdata-similar-to-anndata/3575)

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**Author:** [@christophechu](https://discourse.scverse.org/u/christophechu)\
**Replies:** 1\
**Last updated:** [August 1, 2025, 2:15pm UTC](https://discourse.scverse.org/t/how-to-filter-out-specific-cell-types-in-spatialdata-similar-to-anndata/3575 "2025-08-01T14:15:29Z")

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In anndata, I can easily filter out low-quality cells using the following: adata = adata\[~adata.obs.fine\_celltype.isin(\[‘Low quality’\]), :\].copy() I would like to achieve the same thing in spatialdata, but I’m not sure…

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## [Unexpected DE test results in scvi version 1.3.0 (as compared with version 1.1.2)](https://discourse.scverse.org/t/unexpected-de-test-results-in-scvi-version-1-3-0-as-compared-with-version-1-1-2/3598)

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**Author:** [@jflusche](https://discourse.scverse.org/u/jflusche)\
**Replies:** 15\
**Last updated:** [July 31, 2025, 10:47am UTC](https://discourse.scverse.org/t/unexpected-de-test-results-in-scvi-version-1-3-0-as-compared-with-version-1-1-2/3598 "2025-07-31T10:47:19Z")

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Hello! I recently upgraded scvi from version 1.1.2 to 1.3.0 and attempted to reproduce a one vs all DE test across different cell types. I got drastically different results. I noticed in the release notes that there wer…

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## [Implementing Warmup to a component based on epoch](https://discourse.scverse.org/t/implementing-warmup-to-a-component-based-on-epoch/3736)

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**Author:** [@dbdimitrov](https://discourse.scverse.org/u/dbdimitrov)\
**Replies:** 2\
**Last updated:** [July 31, 2025, 6:43am UTC](https://discourse.scverse.org/t/implementing-warmup-to-a-component-based-on-epoch/3736 "2025-07-31T06:43:05Z")

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Hi, This might be a silly question, but I’m trying to implement a warmup schedule for one of the components of my model. I’ve implemented some make-shift solution, but was hoping to avoid digging through the codebase i…

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## [RESOLVI - continuous\_covariate\_keys](https://discourse.scverse.org/t/resolvi-continuous-covariate-keys/3724)

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**Author:** [@ndove7](https://discourse.scverse.org/u/ndove7)\
**Replies:** 0\
**Last updated:** [July 24, 2025, 7:12pm UTC](https://discourse.scverse.org/t/resolvi-continuous-covariate-keys/3724 "2025-07-24T19:12:37Z")

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Hello, Are there plans to implement the ability to correct using a continuous covariate in RESOLVI like there are in other models? Or is this not possible? Thanks, Nicholas

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