Pixie pipeline described in Liu et al., Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering
☆12Aug 3, 2023Updated 2 years ago
Alternatives and similar repositories for pixie
Users that are interested in pixie are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆12Mar 3, 2023Updated 3 years ago
- ☆71Jan 18, 2023Updated 3 years ago
- End-to-end model for cell segmentation and classification☆22Jan 13, 2025Updated last year
- Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications☆66Mar 14, 2024Updated 2 years ago
- Official repository for Characterization of tumor heterogeneity through segmentation-free representation learning on multiplexed imaging …☆15Sep 28, 2025Updated 7 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆18Apr 5, 2024Updated 2 years ago
- A performant scientific image visualization system.☆36Mar 20, 2026Updated 2 months ago
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆72Nov 4, 2024Updated last year
- Awesome generative spatial omics tools☆26Oct 17, 2025Updated 7 months ago
- ☆14Feb 12, 2026Updated 3 months ago
- Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.☆18Aug 8, 2025Updated 9 months ago
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆17Sep 26, 2021Updated 4 years ago
- Spatial Single-Cell Analysis Toolkit☆111Mar 11, 2026Updated 2 months ago
- Inference code for HoVer-NeXt☆48Oct 26, 2025Updated 6 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆60Jan 9, 2026Updated 4 months ago
- Public EEG-based motor imagery (MI) datasets☆12Feb 1, 2024Updated 2 years ago
- R package for computing Association Plots☆17Nov 4, 2024Updated last year
- Build contrasts for models defined with formulaic☆12Updated this week
- Image Mass Cytometry analysis pipeline☆26Jun 3, 2025Updated 11 months ago
- Camiel's scATAC-seq analysis pipeline☆14Apr 15, 2024Updated 2 years ago
- Histopathology whole slide image library☆16Mar 20, 2026Updated last month
- Access public biological ontologies.☆14Aug 7, 2024Updated last year
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆34Mar 16, 2026Updated 2 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Perturbation-response Score (PS) analysis is a method to quantify diverse perturbation responses and discover novel biological insights i…☆17Apr 20, 2024Updated 2 years ago
- A python implementation of scran computeSumFactors: normalization by deconvolution for single-cell RNA-sequencing☆34Nov 4, 2023Updated 2 years ago
- elliptical fourier descriptors with and without lobe contributions☆13Sep 15, 2020Updated 5 years ago
- multimodal whole slide image registration in a graph structure☆102Jul 4, 2024Updated last year
- Python bindings for SingleR☆16May 6, 2026Updated 2 weeks ago
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆61Aug 17, 2024Updated last year
- Shadow objects for AnnData and MuData (experimental)☆11Feb 28, 2025Updated last year
- Standalone shiny server container for viewing CellChat object☆13Feb 18, 2021Updated 5 years ago
- Identify major cellular signals in bulk transcriptomes☆11Jun 1, 2022Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆11Jan 13, 2020Updated 6 years ago
- ☆34Oct 10, 2025Updated 7 months ago
- ☆50Jun 24, 2022Updated 3 years ago
- FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.☆15Apr 30, 2026Updated 2 weeks ago
- Paired Insertion Counting for snATAC-seq data☆19Mar 15, 2026Updated 2 months ago
- Work with trained factor models in Python☆40Oct 22, 2024Updated last year
- Codes for GFPack++: Attention-Driven Gradient Fields for Optimizing 2D Irregular Packing☆45May 13, 2026Updated last week