CellProfiling / pipexLinks
A pipeline to transform images into valuable analysis items
☆17Updated 6 months ago
Alternatives and similar repositories for pipex
Users that are interested in pipex are comparing it to the libraries listed below
Sorting:
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆39Updated last year
- Spatial Single-Cell Analysis Toolkit☆107Updated last week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆86Updated 2 months ago
- ☆87Updated this week
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆104Updated this week
- Interactive visualization of spatial omics data☆73Updated this week
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆31Updated 2 months ago
- Single-cell spatial proteomics analysis that makes you happy!☆51Updated this week
- A toolkit for processing multiplexed tissue images☆67Updated last month
- comseg☆24Updated 11 months ago
- Interoperability between SpatialData and the Xenium Explorer☆25Updated last year
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆46Updated last year
- Integrated pipeline for multiplexed image analysis☆101Updated last week
- Python package for Probe set selection for targeted spatial transcriptomics.☆48Updated 2 months ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆35Updated last year
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆39Updated 3 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆66Updated last month
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Updated 7 months ago
- Python package for reading imaging mass cytometry (IMC) files☆18Updated this week
- ☆64Updated this week
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆94Updated 2 years ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆112Updated this week
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆82Updated last month
- ☆58Updated last month
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆16Updated 4 years ago
- Spatial analysis of FISH data☆34Updated 7 months ago
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆23Updated 9 months ago
- A probabilistic cell typing algorithm for spatial transcriptomics.☆25Updated 2 months ago
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.☆29Updated 7 months ago
- Multiple-choice microscopy pipeline☆144Updated last month