Www.biorxiv.org (7)#
Bridging Imaging Users to Imaging Analysis - A community survey#
Suganya Sivagurunathan, Stefania Marcotti, Carl J Nelson, Martin L Jones, David J Barry, Thomas J A Slater, Kevin W Eliceiri, Beth A Cimini
Published 2023
Licensed BSD-3-CLAUSE
Tags: Bioimage Analysis, Exclude From Dalia
Content type: Publication, Preprint
CellTrackColab#
Guillaume Jacquemet
Licensed MIT
Tags: Exclude From Dalia
Content type: Notebook, Collection
CytoVI Deep generative modeling of antibody-based single cell technologies#
Florian Ingelfinger, Nathan Levy, Can Ergen, Artemy Bakulin, Alexander Becker, Pierre Boyeau, Martin Kim, Diana Ditz, Jan Dirks, Jonas Maaskola, Tobias Wertheimer, Robert Zeiser, Corinne C. Widmer, Ido Amit, Nir Yosef
Published 2025-09-12
Licensed CC-BY-4.0
CytoVI is a probabilistic generative model that enables statistically rigorous and integrative analysis of antibody-based single cell technologies, outperforming existing methods and enabling key functionalities like cell embeddings and differential protein expression testing, with applications in B cell maturation, non-Hodgkin lymphoma, and diagnostic flow cytometry.
Tags: Artificial Intelligence, Bioinformatics, Include In Dalia
Content type: Preprint
SpatialData: an open and universal data framework for spatial omics#
Luca Marconato, Giovanni Palla, Kevin A Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Marcella Toth, Rahul Shrestha, Harald Vöhringer, Wolfgang Huber, Moritz Gerstung, Josh Moore, Fabian J Theis, Oliver Stegle
Licensed CC-BY-4.0
Tags: Python, Exclude From Dalia
Content type: Publication, Preprint
https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1.abstract
Studentsourcing - aggregating and re-using data from a practical cell biology course#
Joachim Goedhart
Tags: Sharing, Exclude From Dalia
Content type: Preprint
Using Glittr.org to find, compare and re-use online training materials#
Geert van Geest, Yann Haefliger, Monique Zahn-Zabal, Patricia M. Palagi
Licensed CC-BY-4.0
Glittr.org is a platform that aggregates and indexes training materials on computational life sciences from public git repositories, making it easier for users to find, compare, and analyze these resources based on various metrics. By providing insights into the availability of materials, collaboration patterns, and licensing practices, Glittr.org supports adherence to the FAIR principles, benefiting the broader life sciences community.
Tags: Bioimage Analysis, Research Data Management, Exclude From Dalia
Content type: Publication, Preprint
WebAtlas pipeline for integrated single cell and spatial transcriptomic data#
Tong Li, David Horsfall, Daniela Basurto-Lozada
Published 2023-04-28
Licensed None
Single cell and spatial transcriptomics illuminate complementary features of tissues. However, the online dissemination and exploration of multi-modal datasets is challenging. We introduce the WebAtlas pipeline for user-friendly sharing and interactive navigation of integrated datasets. WebAtlas unifies commonly used atlassing technologies into the cloud-optimised Zarr format and builds on Vitessce to enable remote data navigation. We showcase WebAtlas on the developing human lower limb to cross-query cell types and genes across single cell, sequencing- and imaging-based spatial transcriptomic data.
Tags: Spatial Transcriptomics, Single Cell, Bioimage Analysis, Exclude From Dalia
Content type: Collection, Atlas
https://developmental.cellatlas.io/webatlas
https://www.biorxiv.org/content/10.1101/2023.05.19.541329v1