R package for Pathway RespOnsive GENe activity inference

Single-Cell Clustering Assessment Framework

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

Colors for all (R package)

Multiview Intercellular SpaTial modeling framework

End-to-end model for cell segmentation and classification

Gene set scoring for single-cell data

Framework for analysis of cell-types and Ligand-Receptor cooccurrences

Signature Analysis and Visualization for Single-Cell RNA-seq

Repo for webpage with How-To guides for image processing, created by the SCF from the MPI-CBG Dresden.

A python extension for the automatic alignment of a source image or a stack (movie) to a target image/reference frame.

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"

Python module utilizing libCZI for reading Zeiss CZI files.

A simple and easy-to-use Python wrapper for libCZI - a cross-platform C++ library intended for providing read and write access to CZI documents.

Read Carl Zeiss image files (CZI).

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

Code used to benchmark Xenium

Lazy Predict help build a lot of basic models without much code and helps understand which models works better without any parameter tuning

SpatialGlue is a novel deep learning methods for spatial multi-omics data integration.

Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more

StereoMM is a graph fusion model that can integrate gene expression, histological images, and spatial location. And the information interaction within modalities is strengthened by introducing an a…