# Help

**URL:** https://discourse.scverse.org/c/help/27.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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## [About the Help category](https://discourse.scverse.org/t/about-the-help-category/320)

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**Author:** [@adamgayoso](https://discourse.scverse.org/u/adamgayoso)\
**Replies:** 0

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For help with a particular scverse package

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## [Request for an end-to-end ResolVI tutorial on Visium HD cell segmentation data](https://discourse.scverse.org/t/request-for-an-end-to-end-resolvi-tutorial-on-visium-hd-cell-segmentation-data/4060)

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**Author:** [@longyuanshui1231](https://discourse.scverse.org/u/longyuanshui1231)\
**Replies:** 2\
**Last updated:** [October 11, 2026, 4:46pm UTC](https://discourse.scverse.org/t/request-for-an-end-to-end-resolvi-tutorial-on-visium-hd-cell-segmentation-data/4060 "2026-10-11T16:46:04Z")

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Dear ResolVI developers, Thank you for developing such a great tool as ResolVI! I am trying to use ResolVI on my Visium HD data. My data has undergone cell segmentation with ProSeg, but I find the ResolVI tutorials some…

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## [Squidpy calculations on giant data](https://discourse.scverse.org/t/squidpy-calculations-on-giant-data/4041)

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**Author:** [@Sudden\_Deceleration](https://discourse.scverse.org/u/Sudden_Deceleration)\
**Replies:** 1\
**Last updated:** [October 9, 2026, 1:43pm UTC](https://discourse.scverse.org/t/squidpy-calculations-on-giant-data/4041 "2026-10-09T13:43:18Z")

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I only today started looking into spatial analysis and squidpy, so please be patient with me if this has an easy answer. I loaded my data from a whole slide image with 754130 cells, each one carrying a cell type and coo…

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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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## [Aggregating ULM cell-type scores by cluster](https://discourse.scverse.org/t/aggregating-ulm-cell-type-scores-by-cluster/4044)

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**Author:** [@albi](https://discourse.scverse.org/u/albi)\
**Replies:** 1\
**Last updated:** [September 7, 2026, 11:48pm UTC](https://discourse.scverse.org/t/aggregating-ulm-cell-type-scores-by-cluster/4044 "2026-09-07T23:48:35Z")

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Hi! I am using decoupler.mt.ulm with a network of cell-type marker genes to obtain cell-type enrichment scores, basically following the cell-type scoring approach shown in the single-cell enrichment analysis tutorial. I…

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## [Confused by percent\_top purpose in scanpy.pp.calculate\_qc\_metrics](https://discourse.scverse.org/t/confused-by-percent-top-purpose-in-scanpy-pp-calculate-qc-metrics/4032)

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**Author:** [@anjpad](https://discourse.scverse.org/u/anjpad)\
**Replies:** 2\
**Last updated:** [August 19, 2026, 12:35pm UTC](https://discourse.scverse.org/t/confused-by-percent-top-purpose-in-scanpy-pp-calculate-qc-metrics/4032 "2026-08-19T12:35:03Z")

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Hi! As I am a beginner at utilizing scanpy, I would like for someone to better help me understand the purpose of percent\_top when calculating qc metrics. How can adding a percent\_top argument change my preprocessing vs. …

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## [Spatial scatter "library\_id" warning](https://discourse.scverse.org/t/spatial-scatter-library-id-warning/4043)

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**Author:** [@albi](https://discourse.scverse.org/u/albi)\
**Replies:** 0\
**Last updated:** [August 19, 2026, 8:07am UTC](https://discourse.scverse.org/t/spatial-scatter-library-id-warning/4043 "2026-08-19T08:07:17Z")

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Hi! I am working with a CosMx dataset where spatial coordinates are originally defined per FOV. CosMx also provides coordinates transformed into a global coordinate system, which I use to visualize all FOVs belonging to …

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## [How to install solo-sc or use hashsolo from scvi?](https://discourse.scverse.org/t/how-to-install-solo-sc-or-use-hashsolo-from-scvi/1702)

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**Author:** [@hmnzo5gy](https://discourse.scverse.org/u/hmnzo5gy)\
**Replies:** 5\
**Last updated:** [August 18, 2026, 12:23pm UTC](https://discourse.scverse.org/t/how-to-install-solo-sc-or-use-hashsolo-from-scvi/1702 "2026-08-18T12:23:42Z")

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When I attempt to install solo in conda environment lately, I have been encountering the following error. pip install solo-sc Collecting solo-sc Using cached solo-sc-1.3.tar.gz (18 kB) Preparing metadata (setup.py) …

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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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## [Help with cellrank2 macrostates (multiple conditions design)](https://discourse.scverse.org/t/help-with-cellrank2-macrostates-multiple-conditions-design/3978)

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**Author:** [@paolaporracciolo](https://discourse.scverse.org/u/paolaporracciolo)\
**Replies:** 4\
**Last updated:** [July 17, 2026, 9:03am UTC](https://discourse.scverse.org/t/help-with-cellrank2-macrostates-multiple-conditions-design/3978 "2026-07-17T09:03:15Z")

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Hello, I have a question about cellrank2. First off, thank you very much for this very interesting tool. I am currently exploring the trajectories of the differentiation of the respiratory epithelium. The design of the…

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## [Scanpy: use of layers](https://discourse.scverse.org/t/scanpy-use-of-layers/4030)

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**Author:** [@albi](https://discourse.scverse.org/u/albi)\
**Replies:** 3\
**Last updated:** [July 17, 2026, 7:28am UTC](https://discourse.scverse.org/t/scanpy-use-of-layers/4030 "2026-07-17T07:28:17Z")

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Current behavior When working with AnnData.layers, applying a preprocessing transformation and storing the result in a new layer currently requires copying the source layer first and then modifying that copy in place. F…

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## [Within-individual DE/DA with MrVI](https://discourse.scverse.org/t/within-individual-de-da-with-mrvi/4024)

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**Author:** [@mdmanurung](https://discourse.scverse.org/u/mdmanurung)\
**Replies:** 1\
**Last updated:** [July 15, 2026, 8:55am UTC](https://discourse.scverse.org/t/within-individual-de-da-with-mrvi/4024 "2026-07-15T08:55:44Z")

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Hi all, I am running MrVI on data with repeated measures per donor across timepoints. I want to test differential abundance across timepoints while accounting for donor IDs. Current setup\_anndata config: MRVI.setup\_an…

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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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## [mrVI and groupby=None](https://discourse.scverse.org/t/mrvi-and-groupby-none/4017)

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**Author:** [@mmartimis](https://discourse.scverse.org/u/mmartimis)\
**Replies:** 2\
**Last updated:** [June 25, 2026, 6:32am UTC](https://discourse.scverse.org/t/mrvi-and-groupby-none/4017 "2026-06-25T06:32:55Z")

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Hi, I am fairly new to data analysis and therefore there might be an obvious answer to this, but I hope you can help me figure this out. I have a dataset of immune cells with samples from many different predefined dise…

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## ["sd.filter\_by\_table\_query()" fails with "IndexError" on SpatialData 0.7.3 / AnnData 0.12.6](https://discourse.scverse.org/t/sd-filter-by-table-query-fails-with-indexerror-on-spatialdata-0-7-3-anndata-0-12-6/4012)

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**Author:** [@albi](https://discourse.scverse.org/u/albi)\
**Replies:** 6\
**Last updated:** [June 22, 2026, 11:49pm UTC](https://discourse.scverse.org/t/sd-filter-by-table-query-fails-with-indexerror-on-spatialdata-0-7-3-anndata-0-12-6/4012 "2026-06-22T23:49:11Z")

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Hi, I’m encountering an IndexError when using sd.filter\_by\_table\_query() on a SpatialData object. Versions spatialdata: 0.7.3 anndata: 0.12.6 annsel: 0.1.2 Variables print(type(keep\_mask)) \>\<class 'pandas.Series'\> pri…

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## [Hitting API rate limits with cell-annotator](https://discourse.scverse.org/t/hitting-api-rate-limits-with-cell-annotator/4007)

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**Author:** [@fbnrst](https://discourse.scverse.org/u/fbnrst)\
**Replies:** 0\
**Last updated:** [June 11, 2026, 8:43pm UTC](https://discourse.scverse.org/t/hitting-api-rate-limits-with-cell-annotator/4007 "2026-06-11T20:43:29Z")

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I just started trying out cell-annotator. However, I hit rate limits quite quickly. I first tried out the free tier by Anthropic, and then bought 5$ credits, but I keep hitting limits. I wonder what I can do to make this…

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## [Is squidpy co\_occurrence metric symmetric?](https://discourse.scverse.org/t/is-squidpy-co-occurrence-metric-symmetric/3875)

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**Author:** [@ashenflower](https://discourse.scverse.org/u/ashenflower)\
**Replies:** 1\
**Last updated:** [June 10, 2026, 8:03pm UTC](https://discourse.scverse.org/t/is-squidpy-co-occurrence-metric-symmetric/3875 "2026-06-10T20:03:09Z")

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Hello everyone, I’ve recently started using squidpy to analyze my spatial data, and I have a question about the co-occurrence metric. According to the documentation, the co-occurrence is computed as P(A | B) / P(A), wh…

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## [CytoVI took more than 24 hours to train](https://discourse.scverse.org/t/cytovi-took-more-than-24-hours-to-train/3871)

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**Author:** [@ghar1821](https://discourse.scverse.org/u/ghar1821)\
**Replies:** 6\
**Last updated:** [June 10, 2026, 9:47am UTC](https://discourse.scverse.org/t/cytovi-took-more-than-24-hours-to-train/3871 "2026-06-10T09:47:55Z")

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Hi there, I’ve been testing CytoVI ( GitHub - YosefLab/cytovi-reference-implementation )on my data which have a bit over 3.8 million cells. I couldn’t get it to finish the training in 24 hours (I can’t run the job any l…

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## [Confusion on "no IR" definition in scirpy](https://discourse.scverse.org/t/confusion-on-no-ir-definition-in-scirpy/3989)

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**Author:** [@osmanmerdan](https://discourse.scverse.org/u/osmanmerdan)\
**Replies:** 2\
**Last updated:** [May 26, 2026, 6:11pm UTC](https://discourse.scverse.org/t/confusion-on-no-ir-definition-in-scirpy/3989 "2026-05-26T18:11:57Z")

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Hi everyone, In our lab, we use the BD Rhapsody scRNA seq pipeline. Results from our recent CD8+ T cells TCR sequencing analysis confused me regarding the no-IR definition. Here is step-by-step code and sample output #…

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## [Choosing number of latent variables](https://discourse.scverse.org/t/choosing-number-of-latent-variables/4000)

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**Author:** [@Kray](https://discourse.scverse.org/u/Kray)\
**Replies:** 3\
**Last updated:** [May 26, 2026, 3:31pm UTC](https://discourse.scverse.org/t/choosing-number-of-latent-variables/4000 "2026-05-26T15:31:09Z")

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Hi, Is there a way to choose between the number of latent variables when doing scvi integration? Does the hyperparameter tuning provide this option? Thanks, Kamalika

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## [Multiple coordinate systems](https://discourse.scverse.org/t/multiple-coordinate-systems/3999)

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**Author:** [@albi](https://discourse.scverse.org/u/albi)\
**Replies:** 2\
**Last updated:** [May 26, 2026, 1:18pm UTC](https://discourse.scverse.org/t/multiple-coordinate-systems/3999 "2026-05-26T13:18:07Z")

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Hi, I have a Zarr file generated from a CosMx dataset. When I open the object in Napari using napari-spatialdata, I see multiple coordinate systems: The only coordinate system I care about is the global one. The othe…

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## [Grouping/merging CosMx FOVs into cores in SpatialData](https://discourse.scverse.org/t/grouping-merging-cosmx-fovs-into-cores-in-spatialdata/3971)

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**Author:** [@albi](https://discourse.scverse.org/u/albi)\
**Replies:** 6\
**Last updated:** [May 26, 2026, 11:56am UTC](https://discourse.scverse.org/t/grouping-merging-cosmx-fovs-into-cores-in-spatialdata/3971 "2026-05-26T11:56:03Z")

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Hi all and thanks for the awesome Python ecosystem for single-cell and spatial omics data analysis! I’m working with CosMx SpatialData from a TMA experiment, where each core consists of 4–9 FOVs. Currently, each FOV has…

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## [Unable to save subset spatialdata to zarr](https://discourse.scverse.org/t/unable-to-save-subset-spatialdata-to-zarr/3995)

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**Author:** [@npont](https://discourse.scverse.org/u/npont)\
**Replies:** 1\
**Last updated:** [May 21, 2026, 1:34pm UTC](https://discourse.scverse.org/t/unable-to-save-subset-spatialdata-to-zarr/3995 "2026-05-21T13:34:31Z")

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Hello, I have subset a spatialdata using coordinates of a selection. This generated properly a new spatialdata (call it test) containing a subset of the SpatialElements initially present in the whole sdata, as desired. …

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## [Render\_points super pixelized after subsetting SpatialData](https://discourse.scverse.org/t/render-points-super-pixelized-after-subsetting-spatialdata/3994)

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**Author:** [@npont](https://discourse.scverse.org/u/npont)\
**Replies:** 2\
**Last updated:** [May 21, 2026, 11:58am UTC](https://discourse.scverse.org/t/render-points-super-pixelized-after-subsetting-spatialdata/3994 "2026-05-21T11:58:23Z")

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Hello, I cropped my SpatialData object using coordinates (load the coordinates csv with spatialdata\_io.xenium\_explorer\_selection(file) and subset using polygon\_query() ). I then plot the expression of some transcripts …

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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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## [Using curated marker genes together with HVGs for scVI feature selection in adult skeletal muscle snRNA-seq](https://discourse.scverse.org/t/using-curated-marker-genes-together-with-hvgs-for-scvi-feature-selection-in-adult-skeletal-muscle-snrna-seq/3983)

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**Author:** [@p.l.b.chen](https://discourse.scverse.org/u/p.l.b.chen)\
**Replies:** 1\
**Last updated:** [May 12, 2026, 5:43am UTC](https://discourse.scverse.org/t/using-curated-marker-genes-together-with-hvgs-for-scvi-feature-selection-in-adult-skeletal-muscle-snrna-seq/3983 "2026-05-12T05:43:38Z")

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Hi scvi-tools team, I would like to ask whether it is methodologically appropriate to train scVI using a feature set that combines highly variable genes with a small number of curated marker genes. I have been working …

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## [Using ResolVI’s Unsupervised Mode for Cell Annotation](https://discourse.scverse.org/t/using-resolvi-s-unsupervised-mode-for-cell-annotation/3762)

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**Author:** [@qiuzc](https://discourse.scverse.org/u/qiuzc)\
**Replies:** 9\
**Last updated:** [May 7, 2026, 12:36pm UTC](https://discourse.scverse.org/t/using-resolvi-s-unsupervised-mode-for-cell-annotation/3762 "2026-05-07T12:36:53Z")

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Hello, I apologize for reposting here—I initially submitted this as a GitHub issue, but was kindly redirected to ask usage questions on Discourse. I’m working with Xenium spatial transcriptomics data without any prior …

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## [Implementation of PROGENy pathway analysis](https://discourse.scverse.org/t/implementation-of-progeny-pathway-analysis/3972)

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**Author:** [@zanebeckwith](https://discourse.scverse.org/u/zanebeckwith)\
**Replies:** 2\
**Last updated:** [May 1, 2026, 8:19pm UTC](https://discourse.scverse.org/t/implementation-of-progeny-pathway-analysis/3972 "2026-05-01T20:19:47Z")

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Sorry if this is a naive question, but I’m trying to check my understanding of the PROGENy approach to pathway analysis, and scverse/decoupleR’s implementation of it. In the original PROGENy paper, I see that the PROGEN…

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## [Integration challenges in a multi-dataset single cell type maturation atlas](https://discourse.scverse.org/t/integration-challenges-in-a-multi-dataset-single-cell-type-maturation-atlas/3969)

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**Author:** [@grad\_student\_01](https://discourse.scverse.org/u/grad_student_01)\
**Replies:** 2\
**Last updated:** [April 24, 2026, 3:40pm UTC](https://discourse.scverse.org/t/integration-challenges-in-a-multi-dataset-single-cell-type-maturation-atlas/3969 "2026-04-24T15:40:41Z")

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Hi scverse community, I’m building a single-cell maturation atlas integrating 23 publicly available and in-house datasets spanning embryonic day 7.75 through postnatal day 84 in mice (~58,000 cells after QC). I’m runni…

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## [MrVI input and interpretation](https://discourse.scverse.org/t/mrvi-input-and-interpretation/901)

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**Author:** [@Nusob888](https://discourse.scverse.org/u/Nusob888)\
**Replies:** 28\
**Last updated:** [April 23, 2026, 4:42pm UTC](https://discourse.scverse.org/t/mrvi-input-and-interpretation/901 "2026-04-23T16:42:19Z")

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@Justin\_Hong Thanks so much for the MrVI tool and preprint. Really enjoyed reading it. I am just wondering whether the input should be an anndata object of highly variable genes or just the whole cellxgene matrix? I pre…

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