scverse

scverse Conference 2026-10 Copenhagen

Mon, 12 Oct 2026 00:00:00 +0100

Join us for the third scverse conference in Copenhagen (DTU), from Monday, October 12 to Wednesday, October 14, 2026.

Visit the dedicated conference page for more details

Scverse x sc-Proteomics Hackathon 2026-09 Vienna

Fri, 04 Sep 2026 00:00:05 +0100

Welcome

Join us for the joint scverse x single-cell proteomics hackathon on September 4-5, 2026 at the Vienna Biocenter in Vienna.

This hackathon aims to bring together users and developers of scverse tools with mass spectrometry-based single-cell proteomics (SCP) researchers. The main topic of this hackathon will center on the specialized preprocessing and downstream analysis workflows unique to SCP data.

During this hackathon, we will tackle core computational challenges, settle on robust data formats, and establish best practices for handling low-input MS signals. You will have the opportunity to directly improve existing tools, build missing pieces of the ecosystem, and optimize scverse packages for single-cell proteomics data. All contributions will be made publicly available on GitHub under an open-source license.

scverse x Cell Painting Hackathon 2026-09 Berlin

Wed, 02 Sep 2026 00:00:00 +0200

Join us for the scverse × Cell Painting hackathon taking place from Wednesday, September 2 to Friday, September 4 at the Max Delbrück Center, Campus Berlin-Buch, Berlin, Germany.

This hackathon unites the scverse, CytoData Society, and EU-OPENSCREEN communities for three days of collaborative development, bridging scverse and Cell Painting communities at the intersection of image-based profiling, phenomics, and single-cell perturbation analysis.

Visit the dedicated event page for more details

rapids-singlecell 0.15.0: Prebuilt CUDA Wheels and Compiled Kernels

Thu, 30 Apr 2026 00:00:05 +0100

Rapids-singlecell release 0.15.0

We are proud to announce rapids-singlecell release 0.15.0 which comes with lots of new features but also changes to the installation process.

Why the packaging changes

In earlier versions of rapids-singlecell, all GPU kernels were written as CuPy RawKernels. These were compiled the first time you called them — in your environment, on your machine. That worked, but it came with friction:

First-call latency. The initial invocation of a kernel-backed function could take several seconds while nvrtc compiled the CUDA source.
Silent dtype/layout mismatches. A RawKernel receives raw pointers. If the input array had the wrong dtype or wasn’t C-contiguous, the kernel might silently produce garbage rather than raising an error.
CUDA code trapped in Python strings. RawKernels are defined as CUDA source inside Python string literals. That means no syntax highlighting, no autocomplete, and no compiler warnings in your editor — debugging C++ code buried in a Python string is nobody’s idea of a good time.

Starting with 0.15.0, these kernels are compiled once at build time and shipped as nanobind/CUDA C++ extension modules inside the wheel. The result is a more conventional compiled-extension workflow: you pip install the package and every kernel is ready immediately.

scverse Hackathon 2026-03 Berlin

Mon, 30 Mar 2026 00:00:05 +0100

Welcome

Join us for the joint scverse x proteomics hackathon on March 30-31, 2026 at the Max Delbrück Center, Mitte campus in Berlin.

This hackathon aims to bring together users and developers of scverse tools, and proteomics researchers, both imaging and mass spectrometry based. The main topic of this hackathon will be around the preprocessing and analysis of proteomic data, including: multiplex immunofluorescence, liquid-chromatrography mass spectrometry (even single-cell proteomics). During this hackathon, we will discuss approaches, data formats, packages, and best practices; and you will have the opportunity to improve these and the realated code. All contributions will be made publicly available on GitHub under an open source license.

Highlights from the scverse conference 2025

Thu, 20 Nov 2025 00:00:05 -0800

Attendees gather for a group photo at Stanford University

The 2nd scverse conference at Stanford University, Palo Alto, California, on November 17-19, 2025 brought together developers and scientists from academia and industry to discuss the latest advances in computational tools and experimental techniques for single cell and spatial multi omics.

The conference in numbers

The conference in numbers:

scverse Conference 2025-11 Stanford

Mon, 17 Nov 2025 00:00:00 +0100

Join us for the scverse conference taking place from Monday, November 17 to Wednesday, November 19 in Stanford, California.

Visit the dedicated conference page for more details

scverse × BioContextAI: Community Infrastructure for Agentic Analysis

Sat, 08 Nov 2025 00:00:05 +0100

scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We’re excited to announce that we are partnering with BioContextAI, a new open-source initiative for building agentic systems in biomedical research. BioContextAI provides a community registry for Model Context Protocol (MCP) servers. These are standardized tools that allow AI systems to access specialized databases and software. This project was recently published as a Nature Biotechnology correspondence and we are actively starting to explore and contribute scverse MCP servers.

Improved i/o in anndata 0.12

Tue, 29 Jul 2025 10:30:00 +0100

0.12 released

We’re happy to announce that anndata 0.12 is out now! Check out the changelog for a full list of changes. Here, we want to give our users a bit of a deep dive into the new functionality. We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

Zarr v3

Zarr v3 as a file format provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility. Check out the following graphic from the zarr docs: By grouping chunks into shards, which are the individual file units, we can cut down the number of files a given zarr store has. Compare this to zarr v2 where every chunk was its own file! No more file system slowdowns, you can create large zarr stores with no concerns while still retaining the ease of use of zarr.

scverse × Biomni: Agentic Single-Cell Analysis

Mon, 28 Jul 2025 00:00:05 +0100

Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses. Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges. While the scverse ecosystem provides powerful and interoperable tools such as Scanpy, scvi-tools, Squidpy, AnnData, MuData, and SpatialData, researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

Four new scverse core packages

Tue, 01 Jul 2025 00:00:05 +0100

Four new core packages in scverse

We’re happy to announce that four new packages have joined the scverse core ecosystem: SnapATAC2, rapids-singlecell, pertpy, and decoupler. This broadens the scope of scverse beyond our so far supported modalities and brings in new functionality for epigenomics, perturbation screens, GPU acceleration, and functional inference.

Single-cell analysis is evolving rapidly, with new experimental modalities and larger datasets becoming the norm. To keep up with this, we’re expanding scverse to support more domains, more data types, and more scalable computing backends. By bringing these mature, well-maintained tools into the core, we aim to provide a consistent and interoperable foundation across all stages of single-cell analysis.

scverse Hackathon 2025-03 Paris

Mon, 17 Mar 2025 00:00:05 +0100

Welcome

Join us for the joint scverse x Owkin hackathon on March 17-19, 2025 at the Owkin office in Paris.

This hackathon aims to bring together users and developers of scverse tools, researchers, and owkinautes. The main topic of this hackathon will be spatial transcriptomics. During this hackathon, you will have the opportunity to improve existing code bases and add new features to scverse tools. All contributions will be made publicly available on GitHub under an open source license.

Highlights from the inaugural scverse conference

Thu, 14 Nov 2024 00:00:05 +0100

The first scverse conference, held in Munich, Germany from 10-12 September, 2024 brought together leading scientists, developers, and researchers from the single-cell genomics and spatial biology community. The conference was organized around five main events: (A) 6 keynotes from leaders in the field (B) 13 short talks from developers, graduate students, postdocs (C) 14 workshops with hands-on experience on various aspects of data analysis and software development (D) Poster session showcasing more than 50 posters (E) Talks from our sponsors showcasing their latest advancements. This year, the focus was on latest community-driven developments in multi-modal and spatial data analysis, broadening scverse accessibility and outreach, and enhancing interoperability. With over 170 participants from 17 different countries, the inaugural scverse conference was a success. Here, we provide major highlights from the conference.

scverse Conference 2024-09 Munich

Tue, 10 Sep 2024 00:00:05 +0100

Join us for the first scverse conference taking place from Tuesday, September 10 to Thursday, September 12 in Munich, Germany. Stay tuned for the registrations, speaker announcements, and more!

Visit the dedicated conference page for more details

scverse Hackathon 2024-04 Boston

Tue, 02 Apr 2024 00:00:05 +0100

Welcome

Join us for the scverse Hackathon taking place from Tuesday, April 2nd, 09:00 AM to Thursday, April 4th, 06:00 PM at Harvard Medical School (Boston, MA).

The scverse hackathon is free. Local and international attendees could register through an open application. More information can be found at the website

Hackathon Tasks

Visualizing remote SpatialData Zarr datasets with Vitessce
Unified plotting for SpatialData: static, Napari, Vitessce
Pseudotime trajectory explorer widget in Jupyter based on jupyter-scatter
Genomic range DataFrame operations in scverse with genomic-features and bioframe
Better interactive widgets for scverse with anywidget

scverse Hackathon 2023-11 Cambridge

Sun, 26 Nov 2023 00:00:05 +0100

Welcome

Join us for the scverse Hackathon taking place from Monday, November 27th, 9:00 AM to Wednesday, November 29th, afternoon at Wellcome Genome Campus ((Hinxton CB10 1SA, Cambridge, UK)).

The scverse hackathon is free. Local and international attendees could register through an open application.

Hackathon Focus Areas

Multi-condition analysis - Improve tools for analysis, visualization & tutorials for comparative analysis of single-cell datasets.
Data 4 AI - writing new packages and docs for pytorch data loaders for single-cell omics datasets from scverse data objects
scverse template repos - improvements to scverse cookiecutter templates for tools and analysis repos

An overview of the outcomes of the hackathon can be found here.

scverse Hackathon 2023-04 Heidelberg

Wed, 26 Apr 2023 00:00:05 +0100

Welcome

Join us for the scverse Hackathon taking place from Wednesday, April 26th, 12:00 PM to Friday, April 28th, afternoon at BioQuant (Neuenheimer Feld 267, 69120 Heidelberg, Germany).

The scverse hackathon is free. The event was invite only. We will try to make future editions open to everyone.

Event Schedule

Wednesday, April 26th (SR041)
- 13:30 – 14:00 — PI introductions (Julio Saez-Rodriguez, Wolfgang Huber)
- 14:00 – 14:30 — Hackathon introduction
- 14:30 – 15:00 — State of the scverse + Q&A
- 15:00 – 15:30 — Coffee break
- 15:30 – 18:30 — Split into groups and hack
- 18:30 – 19:00 — Short updates from teams
Thursday, April 27th (SR042 & SR044)

scverse Hackathon 2022-12 Innsbruck

Thu, 08 Dec 2022 00:00:05 +0100

Welcome

Join us for the scverse Hackathon taking place from Thursday, December 8th, 10:00 AM to Friday, December 9th, afternoon In Innsbruck. The scverse hackathon is free. The event was invite only. We will try to make future editions open to everyone.

Hackathon checklist

Check that you agree with the scverse code of conduct.
Ensure that you have a Github account.
Join our zulip where you’ll be added to the hackathon stream. Say hi if this is your first time on the scverse zulip!
Have python and any scverse package that you might work on installed.

Hello world

Tue, 17 May 2022 00:00:05 +0100

Due to the increasing reliance of scientific research on complex computational pipelines, foundational software in the life sciences has outgrown individual labs and institutes in terms of its scale and impact. This has motivated us to start something more than a code repository for an exciting new project – a new consortium to organize and support core (mostly) Python tools for single cell life science research. We are excited to announce scverse.

scverse Hackathon 2022-05 Munich

Mon, 02 May 2022 00:00:05 +0100

Welcome

Join us for the scverse Hackathon taking place from Monday, May 2nd, 9:00 AM to Tuesday, May 3rd, afternoon In Munich. The scverse hackathon is free. The event was invite only. We will try to make future editions open to everyone.

Hackathon checklist

Check that you agree with the scverse code of conduct.
Ensure that you have a Github account.
Join our zulip where you’ll be added to the hackathon stream. Say hi if this is your first time on the scverse zulip!
Have python and any scverse package that you might work on installed.

scverse conference 2025

Mon, 01 Jan 0001 00:00:00 +0000

scverse conference 2026

Mon, 01 Jan 0001 00:00:00 +0000