A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.

Multiple Fill, Color and Other Scales in `ggplot2`

BANKSY: spatial clustering

Advanced Normalization Tools (ANTs)

Code for ColabDock paper

An open and interoperable data framework for spatial omics data

Raw format to OME-TIFF converter

A tiny Python library for writing multi-channel TIFF stacks.

Bio-Formats image file format to raw format converter

Easy interactive web applications with R

Morphological snakes for image segmentation and tracking

a minimal, scriptable genome browser for python

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

dcHiC: Differential compartment analysis for Hi-C datasets

LPIPS metric. pip install lpips

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Utils and convenience functions for large-scale bio-image analysis.

GPT4All: Run Local LLMs on Any Device. Open-source and available for commercial use.

A fast, simple & powerful blog framework, powered by Node.js.

tools for finding discrete bright spots in images (for multiplexed FISH, includes background subtraction, deconv, and blob detection)

Image processing in Python

Circular visualization in R

Analyzing cellular niches in spatial transcriptomics data

Toolbox for the analysis of smFISH images.

Feature extraction from GEOJson nuclei and tissue segmentation maps

ClusterMap for multi-scale clustering analysis of spatial gene expression