# General

**URL:** https://discourse.scverse.org/c/general/21.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 General category](https://discourse.scverse.org/t/about-the-general-category/136)

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

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Use this for topics broader in scope than one particular package.

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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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## [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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## [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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## [Using Marimo with SpatialData](https://discourse.scverse.org/t/using-marimo-with-spatialdata/3973)

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**Author:** [@albi](https://discourse.scverse.org/u/albi)\
**Replies:** 0\
**Last updated:** [April 30, 2026, 7:28pm UTC](https://discourse.scverse.org/t/using-marimo-with-spatialdata/3973 "2026-04-30T19:28:08Z")

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Hi all, I’ve been experimenting with Marimo recently and appreciate its reactive, immutable execution model. However, I’m running into some friction when trying to use it together with SpatialData. A lot of typical wor…

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## [Inferring whether a particular disease is closer to other?](https://discourse.scverse.org/t/inferring-whether-a-particular-disease-is-closer-to-other/3937)

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**Author:** [@Indianhedgehog](https://discourse.scverse.org/u/Indianhedgehog)\
**Replies:** 1\
**Last updated:** [February 19, 2026, 3:01pm UTC](https://discourse.scverse.org/t/inferring-whether-a-particular-disease-is-closer-to-other/3937 "2026-02-19T15:01:57Z")

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Hi everyone, I have integrated single cells from different diseases. I want to calculate which disease is closer to my disease of interest in terms of gene expression? I have looked up online regarding this, but didn’t m…

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## [What to do with small clusters outside larger clusters in UMAP? Remove or keep?](https://discourse.scverse.org/t/what-to-do-with-small-clusters-outside-larger-clusters-in-umap-remove-or-keep/3935)

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**Author:** [@mmartimis](https://discourse.scverse.org/u/mmartimis)\
**Replies:** 2\
**Last updated:** [February 10, 2026, 10:00am UTC](https://discourse.scverse.org/t/what-to-do-with-small-clusters-outside-larger-clusters-in-umap-remove-or-keep/3935 "2026-02-10T10:00:54Z")

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Hi, I have a UMAP that is generally nicely clustered (with Harmony), but there are areas where I get long “tendrils” sticking out of the clusters or just spots of smaller clusters. What do you suggest doing with these? …

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## [\[Tool\] scVAE-Annotator: Automated Cell Type Annotation for scRNA-seq with VAE and Adaptive Marker Discovery](https://discourse.scverse.org/t/tool-scvae-annotator-automated-cell-type-annotation-for-scrna-seq-with-vae-and-adaptive-marker-discovery/3919)

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**Author:** [@or4k2l](https://discourse.scverse.org/u/or4k2l)\
**Replies:** 7\
**Last updated:** [February 4, 2026, 7:03am UTC](https://discourse.scverse.org/t/tool-scvae-annotator-automated-cell-type-annotation-for-scrna-seq-with-vae-and-adaptive-marker-discovery/3919 "2026-02-04T07:03:23Z")

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Hi community, I’d like to share scVAE-Annotator, a Python pipeline for automated cell type annotation in single-cell RNA-seq data that addresses common challenges in cell type identification. Key Features: VAE-based d…

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

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

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

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## [Clarification on the random variable W in the decoder](https://discourse.scverse.org/t/clarification-on-the-random-variable-w-in-the-decoder/3860)

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**Author:** [@jcara514](https://discourse.scverse.org/u/jcara514)\
**Replies:** 2\
**Last updated:** [November 11, 2025, 1:33pm UTC](https://discourse.scverse.org/t/clarification-on-the-random-variable-w-in-the-decoder/3860 "2025-11-11T13:33:45Z")

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Hello, So I’ve been doing a deep dive into the technical aspects of this software for my dissertation project. Something that I noticed while going through the decoder algorithm was the following: w is defined as Gamma(…

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## [MultiVI questions on Integrating Multiple Multiome Datasets](https://discourse.scverse.org/t/multivi-questions-on-integrating-multiple-multiome-datasets/3786)

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**Author:** [@DineshRavindraRaju](https://discourse.scverse.org/u/DineshRavindraRaju)\
**Replies:** 1\
**Last updated:** [September 25, 2025, 12:33pm UTC](https://discourse.scverse.org/t/multivi-questions-on-integrating-multiple-multiome-datasets/3786 "2025-09-25T12:33:02Z")

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Hi all, I have a couple of questions regarding the tool. First, thank you for providing both the tool. For multiple multiome samples, is it better to use Cell Ranger aggr without normalization to integrate modalities …

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## [Preparing adata.uns for cellflow](https://discourse.scverse.org/t/preparing-adata-uns-for-cellflow/3776)

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**Author:** [@WeihangChen0](https://discourse.scverse.org/u/WeihangChen0)\
**Replies:** 0\
**Last updated:** [August 13, 2025, 10:27pm UTC](https://discourse.scverse.org/t/preparing-adata-uns-for-cellflow/3776 "2025-08-13T22:27:23Z")

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Dear scverse community, I’m learning the new cellflow framework for modeling perturbation with other covariates(such as donor) via the tutorial using cytokines on PBMCs( Predicting donor-specific cytokine effects on PBM…

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## [How to run cellflow faster?](https://discourse.scverse.org/t/how-to-run-cellflow-faster/3770)

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**Author:** [@Zhixuan-Jing](https://discourse.scverse.org/u/Zhixuan-Jing)\
**Replies:** 0\
**Last updated:** [August 7, 2025, 12:42pm UTC](https://discourse.scverse.org/t/how-to-run-cellflow-faster/3770 "2025-08-07T12:42:11Z")

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I want to run through cell flow on a tiny dataset with couple of minutes with my laptop give n that the dataset is small enough, but it still takes several hours even if tqdm shows 1.15it/s (I set 100 iterations) and sti…

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## [Harmony-R vs Harmony-Py](https://discourse.scverse.org/t/harmony-r-vs-harmony-py/3738)

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**Author:** [@Hrovatin](https://discourse.scverse.org/u/Hrovatin)\
**Replies:** 0\
**Last updated:** [July 31, 2025, 2:14pm UTC](https://discourse.scverse.org/t/harmony-r-vs-harmony-py/3738 "2025-07-31T14:14:45Z")

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Hi, A while ago Amir Ali Moinfar (and me) compared Harmony from R and the python implementation. We actually observed that the python implementation generally performed better, with higher biological preservation within…

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## [Deconvolute spatial transcriptomics (visium) with unannotated single-cell (10x)](https://discourse.scverse.org/t/deconvolute-spatial-transcriptomics-visium-with-unannotated-single-cell-10x/3694)

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**Author:** [@cell\_kc](https://discourse.scverse.org/u/cell_kc)\
**Replies:** 3\
**Last updated:** [July 10, 2025, 8:10am UTC](https://discourse.scverse.org/t/deconvolute-spatial-transcriptomics-visium-with-unannotated-single-cell-10x/3694 "2025-07-10T08:10:36Z")

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I have a spatial transcriptomics dataset (10x visium) of a tumour microarray and some of the samples have matched single-cell RNA-seq data (10x). I would like to annotate my spatial data with the single-cell data. Howeve…

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## [Cellxgene datasets raw data? scaled?](https://discourse.scverse.org/t/cellxgene-datasets-raw-data-scaled/3705)

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**Author:** [@LysSanzMoreta](https://discourse.scverse.org/u/LysSanzMoreta)\
**Replies:** 2\
**Last updated:** [July 8, 2025, 9:56am UTC](https://discourse.scverse.org/t/cellxgene-datasets-raw-data-scaled/3705 "2025-07-08T09:56:02Z")

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Hi! First, I would just like to know how were the .X matrices in the .h5ad files that can be downloaded from Datasets - CZ CELLxGENE Discover made ? What is the origin of those floats? I finally found that the raw da…

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## [Regressing out isotype controls](https://discourse.scverse.org/t/regressing-out-isotype-controls/346)

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**Author:** [@FelixTheStudent](https://discourse.scverse.org/u/FelixTheStudent)\
**Replies:** 4\
**Last updated:** [June 6, 2025, 2:44am UTC](https://discourse.scverse.org/t/regressing-out-isotype-controls/346 "2025-06-06T02:44:54Z")

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Hi scvi-tools team, thanks for the great work so far! I’d like a recommendation on whether to regress out isotype controls or not. Simply excluding them from analysis does not seem sufficient, because \> 10 actual prote…

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## [Tutorial Scanpy X ReadStore Integration for NGS Project Management](https://discourse.scverse.org/t/tutorial-scanpy-x-readstore-integration-for-ngs-project-management/3510)

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**Author:** [@JonathanA](https://discourse.scverse.org/u/JonathanA)\
**Replies:** 0\
**Last updated:** [February 25, 2025, 4:16pm UTC](https://discourse.scverse.org/t/tutorial-scanpy-x-readstore-integration-for-ngs-project-management/3510 "2025-02-25T16:16:44Z")

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Hi there, I wanted to leave there a short tutorial we created illustrating how to combine the ReadStore database for NGS project management with scanpy for building scalable workflow. Best wishes.

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## [How to concatenate andata objects when you have citeseq data](https://discourse.scverse.org/t/how-to-concatenate-andata-objects-when-you-have-citeseq-data/3403)

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**Author:** [@bioinf](https://discourse.scverse.org/u/bioinf)\
**Replies:** 5\
**Last updated:** [January 29, 2025, 4:29pm UTC](https://discourse.scverse.org/t/how-to-concatenate-andata-objects-when-you-have-citeseq-data/3403 "2025-01-29T16:29:14Z")

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Hello, I have .h5 files that contain gene expression and cite seq data. I am trying to confirm that the way I imported them seems correct: Sample1 = sc.read\_10x\_h5(‘E:\\Sample1\_filtered\_feature\_bc\_matrix.h5’, gex\_only=F…

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## [Does the order of HTOs matter?](https://discourse.scverse.org/t/does-the-order-of-htos-matter/3410)

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**Author:** [@bioinf](https://discourse.scverse.org/u/bioinf)\
**Replies:** 0\
**Last updated:** [January 7, 2025, 8:37pm UTC](https://discourse.scverse.org/t/does-the-order-of-htos-matter/3410 "2025-01-07T20:37:15Z")

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Hello, I am using scanpy.external.pp.hashsolo to demultiplex my samples based on hashtags. However, I noticed that if I put the HTOs in different order I get slightly different results. Is that expected behavior? sce.p…

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## [Looking for Pseudobulk Methods](https://discourse.scverse.org/t/looking-for-pseudobulk-methods/3341)

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**Author:** [@victorsanchezarevalo](https://discourse.scverse.org/u/victorsanchezarevalo)\
**Replies:** 1\
**Last updated:** [November 17, 2024, 4:53pm UTC](https://discourse.scverse.org/t/looking-for-pseudobulk-methods/3341 "2024-11-17T16:53:52Z")

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I’m exploring new ways to generate pseudobulk data that better reflect biological reality. Most approaches I’ve found in the literature, or in commonly used packages, rely on simply summing or averaging single-cell expre…

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## [How to load GEO datasets for analysis using Scanpy / Scvi tools?](https://discourse.scverse.org/t/how-to-load-geo-datasets-for-analysis-using-scanpy-scvi-tools/800)

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**Author:** [@mostafa-ti](https://discourse.scverse.org/u/mostafa-ti)\
**Replies:** 6\
**Last updated:** [November 6, 2024, 5:24am UTC](https://discourse.scverse.org/t/how-to-load-geo-datasets-for-analysis-using-scanpy-scvi-tools/800 "2024-11-06T05:24:25Z")

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I have a question about data export from GEO to scanpy object. I want to make GSE81608 dataset into scanpy object file. (GEO Accession viewer) Usually I make scanpy object by 3 files (barcodes, features, matrix) but GS…

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## [Gene Regulatory Network in scverse](https://discourse.scverse.org/t/gene-regulatory-network-in-scverse/953)

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**Author:** [@sim](https://discourse.scverse.org/u/sim)\
**Replies:** 2\
**Last updated:** [October 20, 2024, 7:35pm UTC](https://discourse.scverse.org/t/gene-regulatory-network-in-scverse/953 "2024-10-20T19:35:35Z")

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Dear all, I was wondering if you have any pointers towards Gene Regulatory Network Analysis tools compatible with scverse (basically python based). Ideally, I would like to tap into both, single-cell and spatial transcr…

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## [\[suggestion\] what would be the appropriate pipeline to perform joint embedding of GEX and ATAC?](https://discourse.scverse.org/t/suggestion-what-would-be-the-appropriate-pipeline-to-perform-joint-embedding-of-gex-and-atac/3275)

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**Author:** [@yojetsharma](https://discourse.scverse.org/u/yojetsharma)\
**Replies:** 1\
**Last updated:** [October 17, 2024, 1:09am UTC](https://discourse.scverse.org/t/suggestion-what-would-be-the-appropriate-pipeline-to-perform-joint-embedding-of-gex-and-atac/3275 "2024-10-17T01:09:33Z")

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I have processed my snRNA of multiome using scanpy and snATAC using snapatac2. Both have been annotated as well. I would like to perform joint embedding of rna and atac but the var attributes are different and so are th…

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## [Release of scvi-tools version 1.2](https://discourse.scverse.org/t/release-of-scvi-tools-version-1-2/2446)

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**Author:** [@Yun-Ching-Chen](https://discourse.scverse.org/u/Yun-Ching-Chen)\
**Replies:** 1\
**Last updated:** [August 26, 2024, 5:28pm UTC](https://discourse.scverse.org/t/release-of-scvi-tools-version-1-2/2446 "2024-08-26T17:28:02Z")

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Hi, I came across the MrVI paper and found it looks a very promising method. I want to test it but its github version is currently deprecated while the latest version of scvi-tools (v1.2) which contains MrVI is not rele…

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## [ST: clustering on each tissue section or clustering on all combined in anndata object?](https://discourse.scverse.org/t/st-clustering-on-each-tissue-section-or-clustering-on-all-combined-in-anndata-object/2460)

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**Author:** [@IbrahimFangary](https://discourse.scverse.org/u/IbrahimFangary)\
**Replies:** 0\
**Last updated:** [August 19, 2024, 6:44pm UTC](https://discourse.scverse.org/t/st-clustering-on-each-tissue-section-or-clustering-on-all-combined-in-anndata-object/2460 "2024-08-19T18:44:27Z")

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I’m new to MERFISH spatial transcriptomics and wondering whether I should preprocess and cluster cells for each tissue section separately or combine all the tissue sections into a single AnnData object for preprocessing …

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## [Teaching resources relating to scverse ecosystem?](https://discourse.scverse.org/t/teaching-resources-relating-to-scverse-ecosystem/2454)

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**Author:** [@munfred](https://discourse.scverse.org/u/munfred)\
**Replies:** 0\
**Last updated:** [August 17, 2024, 11:15am UTC](https://discourse.scverse.org/t/teaching-resources-relating-to-scverse-ecosystem/2454 "2024-08-17T11:15:53Z")

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Dear scverse community, my name is Eduardo, I am a new assistant professor in computational biology at Mohamed bin Zayed University of Artificial Intelligence (MBZUAI), a new graduate-level research university in Abu Dha…

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## [Questions about how to do DE with one replicate for one sample](https://discourse.scverse.org/t/questions-about-how-to-do-de-with-one-replicate-for-one-sample/2421)

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**Author:** [@Rsugihara01](https://discourse.scverse.org/u/Rsugihara01)\
**Replies:** 0\
**Last updated:** [July 31, 2024, 9:17am UTC](https://discourse.scverse.org/t/questions-about-how-to-do-de-with-one-replicate-for-one-sample/2421 "2024-07-31T09:17:29Z")

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Hello, thank you for providing such brilliant tools! I am new to analyzing my scRNAseq datasets, and I would like some advice on how to perform DE (differential expression) analysis. My dataset contains cells from two …

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## [Give your feedback on new visualization tools for Spatial data…](https://discourse.scverse.org/t/give-your-feedback-on-new-visualization-tools-for-spatial-data/2396)

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**Author:** [@ryan](https://discourse.scverse.org/u/ryan)\
**Replies:** 1\
**Last updated:** [July 25, 2024, 8:23pm UTC](https://discourse.scverse.org/t/give-your-feedback-on-new-visualization-tools-for-spatial-data/2396 "2024-07-25T20:23:26Z")

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Give your feedback on new visualization tools for Spatial data… Hi, I’m Ryan and I work at the Chan Zuckerberg Initiative building tools that help single cell biologists explore data. The Cell Science team at the Chan Z…

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## [Filtering by coordinate system](https://discourse.scverse.org/t/filtering-by-coordinate-system/2270)

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**Author:** [@nazim](https://discourse.scverse.org/u/nazim)\
**Replies:** 0\
**Last updated:** [May 12, 2024, 7:04am UTC](https://discourse.scverse.org/t/filtering-by-coordinate-system/2270 "2024-05-12T07:04:18Z")

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Hi Guys, I tried to follow the tutorial about the filtering by coordinate system in Napari Spatial Data: Spatial query — spatialdata So, here is my dataset: SpatialData object with: ├── Images │ ├── 'v1\_hires\_imag…

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