PreibischLab / STIM
Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.
☆26Updated 3 weeks ago
Related projects ⓘ
Alternatives and complementary repositories for STIM
- Tool for precise, interactive, fast and scalable FISH spot detection☆46Updated 2 months ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆35Updated last year
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆25Updated last week
- A plugin to visualise 3D spatial single cell omics☆21Updated 7 months ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆24Updated last month
- Minimum Information about Tissue Imaging☆20Updated last year
- Interactive visualization of spatial omics data☆41Updated this week
- ☆23Updated last month
- ☆28Updated 10 months ago
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆49Updated 5 months ago
- ☆29Updated 6 months ago
- ☆28Updated 3 weeks ago
- ☆12Updated 2 months ago
- Spatial Single-Cell Analysis Toolkit☆74Updated 2 months ago
- ☆43Updated last week
- ☆38Updated last week
- A probabilistic cell typing algorithm for spatial transcriptomics.☆23Updated this week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆70Updated this week
- MERFISH decoding software☆24Updated last year
- Graph-based Decoding for In Situ Sequencing☆10Updated 4 years ago
- Interoperability between SpatialData and the Xenium Explorer☆15Updated 3 months ago
- ☆33Updated 7 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆29Updated 6 months ago
- Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"☆10Updated last year
- Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images☆13Updated this week
- Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.☆15Updated last week
- Image Processing Package for the Paper "Self-organization and symmetry breaking in intestinal organoid development"☆11Updated 4 years ago
- Image registration (alignment) software for large microscopy images☆21Updated last year
- Integrated pipeline for multiplexed image analysis☆75Updated this week
- ☆14Updated this week