# Latest

**URL:** https://discourse.scverse.org/latest.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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## [Welcome to the scverse discourse!](https://discourse.scverse.org/t/welcome-to-the-scverse-discourse/7)

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**Author:** [@system](https://discourse.scverse.org/u/system)\
**Replies:** 0\
**Last updated:** [October 19, 2020, 6:30pm UTC](https://discourse.scverse.org/t/welcome-to-the-scverse-discourse/7 "2020-10-19T18:30:59Z")

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Please use this forum to ask questions about any scverse packages, get help with specific code and discuss novel ideas. Bug reports should go to the issues of the respective package. Please also familiarize yourself wi…

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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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## [Pbcheck 0.1.0: a CLI that audits a scRNA-seq DE design for pseudoreplication](https://discourse.scverse.org/t/pbcheck-0-1-0-a-cli-that-audits-a-scrna-seq-de-design-for-pseudoreplication/4047)

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**Author:** [@Genn](https://discourse.scverse.org/u/Genn)\
**Replies:** 0\
**Last updated:** [September 7, 2026, 1:29am UTC](https://discourse.scverse.org/t/pbcheck-0-1-0-a-cli-that-audits-a-scrna-seq-de-design-for-pseudoreplication/4047 "2026-09-07T01:29:12Z")

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I released pbcheck 0.1.0, a Python package and command-line tool that audits a single-cell RNA-seq differential-expression design for pseudoreplication. You give it one .h5ad file, the donor and condition columns, and t…

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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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## [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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## [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:** 0\
**Last updated:** [August 4, 2026, 11:16am UTC](https://discourse.scverse.org/t/squidpy-calculations-on-giant-data/4041 "2026-08-04T11:16:59Z")

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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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## [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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## [Computer systems specifications for million-cell datasets](https://discourse.scverse.org/t/computer-systems-specifications-for-million-cell-datasets/4038)

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**Author:** [@urjabhatt](https://discourse.scverse.org/u/urjabhatt)\
**Replies:** 0\
**Last updated:** [July 28, 2026, 1:36am UTC](https://discourse.scverse.org/t/computer-systems-specifications-for-million-cell-datasets/4038 "2026-07-28T01:36:32Z")

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I am curious what computer systems or cloud systems (specifications) do people use for processing large-scale single cell (~million cells) datasets. Any recommendations are appreciated.

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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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## [metal-SingleCell — a work-in-progress Metal/MLX port of rapids-singlecell for Apple Silicon (feedback welcome)](https://discourse.scverse.org/t/metal-singlecell-a-work-in-progress-metal-mlx-port-of-rapids-singlecell-for-apple-silicon-feedback-welcome/4018)

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**Author:** [@gingerii](https://discourse.scverse.org/u/gingerii)\
**Replies:** 1\
**Last updated:** [July 15, 2026, 6:48am UTC](https://discourse.scverse.org/t/metal-singlecell-a-work-in-progress-metal-mlx-port-of-rapids-singlecell-for-apple-silicon-feedback-welcome/4018 "2026-07-15T06:48:21Z")

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TL;DR: I’ve been working on an independent Metal/MLX re-implementation of rapids-singlecell so the scanpy/squidpy GPU workflow can run on the Apple M-series GPU. It’s a drop-in API and covers ~30 pp/tl/gr functions, vali…

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## [Proposal: Add TAU Community Detection as a clustering method for Scanpy / scverse ecosystem](https://discourse.scverse.org/t/proposal-add-tau-community-detection-as-a-clustering-method-for-scanpy-scverse-ecosystem/3887)

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**Author:** [@HillelCharbit](https://discourse.scverse.org/u/HillelCharbit)\
**Replies:** 6\
**Last updated:** [July 14, 2026, 1:01pm UTC](https://discourse.scverse.org/t/proposal-add-tau-community-detection-as-a-clustering-method-for-scanpy-scverse-ecosystem/3887 "2026-07-14T13:01:59Z")

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Hi everyone, I would like to propose adding a new clustering method to the scverse ecosystem (potentially as a Scanpy plugin, or as a built-in Scanpy tool). The method is called TAU Community Detection, a genetic-algori…

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## [CellRank for multiome blood development](https://discourse.scverse.org/t/cellrank-for-multiome-blood-development/4023)

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**Author:** [@mike\_martinez99](https://discourse.scverse.org/u/mike_martinez99)\
**Replies:** 0\
**Last updated:** [July 8, 2026, 2:23pm UTC](https://discourse.scverse.org/t/cellrank-for-multiome-blood-development/4023 "2026-07-08T14:23:24Z")

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Hello, I have zebrafish multiome data for a developmental blood system. My data is 6 timepoints ranging from 12hpf to 30hpf for blood and vasculature populations. The data has been integrated in Seurat and ran through m…

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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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## [Quick question from the Awkward Array project](https://discourse.scverse.org/t/quick-question-from-the-awkward-array-project/4001)

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**Author:** [@ianna](https://discourse.scverse.org/u/ianna)\
**Replies:** 3\
**Last updated:** [June 9, 2026, 5:46am UTC](https://discourse.scverse.org/t/quick-question-from-the-awkward-array-project/4001 "2026-06-09T05:46:56Z")

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Hi all, I’m the maintainer of Awkward Array, and I noticed that your team has been exploring or integrating Awkward alongside AnnData. It’s incredibly exciting to see the library finding a home in single-cell workflows. …

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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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