Pinned Repositories
2023_EMBL_Rome_training
matreial for EMBO Rome image analysis training
hcs_analysis
microaligner
Image registration (alignment) software for large microscopy images
to_ome_tif
nextflow DSL2 pipeline (leveraging /[raw2ometiff](https://github.com/glencoesoftware/raw2ometiff)) to convert almost any images to ome.tiff/ome.zarr
workflow-decoding
Decoding of image-based spatial transcriptomics
workflow-registration
workflow-segmentation
workflow-stitching
MAARS
Fiji/Micro-Manager plugin for Mitotic Analysis And Recording System
webatlas-pipeline
A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
BioinfoTongLI's Repositories
BioinfoTongLI/to_ome_tif
nextflow DSL2 pipeline (leveraging /[raw2ometiff](https://github.com/glencoesoftware/raw2ometiff)) to convert almost any images to ome.tiff/ome.zarr
BioinfoTongLI/workflow-registration
BioinfoTongLI/workflow-segmentation
BioinfoTongLI/2023_EMBL_Rome_training
matreial for EMBO Rome image analysis training
BioinfoTongLI/hcs_analysis
BioinfoTongLI/microaligner
Image registration (alignment) software for large microscopy images
BioinfoTongLI/workflow-decoding
Decoding of image-based spatial transcriptomics
BioinfoTongLI/workflow-stitching
BioinfoTongLI/apoc
Accelerated Pixel and Object Classifiers (APOC)
BioinfoTongLI/BaSiCPy
BioinfoTongLI/Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
BioinfoTongLI/cell2location
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
BioinfoTongLI/codeocean-webatlas
BioinfoTongLI/containers
BioinfoTongLI/ELD
BioinfoTongLI/fractal-tasks-core
Main tasks for the Fractal analytics platform
BioinfoTongLI/Image-ST
A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode
BioinfoTongLI/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
BioinfoTongLI/nextflow-modules
nf-core-compatible modules for Nextflow
BioinfoTongLI/nf-core-configs
Config files used to define parameters specific to compute environments at different Institutions
BioinfoTongLI/planer-nf
BioinfoTongLI/postcode
Decoding of image-based spatial transcriptomics
BioinfoTongLI/spatial_annot
BioinfoTongLI/spatialdata-io
BioinfoTongLI/tools-docker
All my CLI tools wrapped in Docker
BioinfoTongLI/vim_config
My personal vim configuration
BioinfoTongLI/vitessce
Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
BioinfoTongLI/webatlas-pipeline
BioinfoTongLI/workflow-assign-peaks-to-cells
BioinfoTongLI/workflow-xenium