BioinfoTongLI

to_ome_tif

nextflow DSL2 pipeline (leveraging /[raw2ometiff](https://github.com/glencoesoftware/raw2ometiff)) to convert almost any images to ome.tiff/ome.zarr

workflow-registration

workflow-segmentation

2023_EMBL_Rome_training

matreial for EMBO Rome image analysis training

hcs_analysis

microaligner

Image registration (alignment) software for large microscopy images

workflow-decoding

Decoding of image-based spatial transcriptomics

workflow-stitching

ashlar

ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

apoc

Accelerated Pixel and Object Classifiers (APOC)

BaSiCPy

Baysor

Bayesian Segmentation of Spatial Transcriptomics Data

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

codeocean-webatlas

containers

fractal-tasks-core

Main tasks for the Fractal analytics platform

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

nf-core-configs

Config files used to define parameters specific to compute environments at different Institutions

planer-nf

postcode

Decoding of image-based spatial transcriptomics

spatial_annot

spatialdata

Spatial Data

spatialdata-io

spatialdata-sandbox

tools-docker

All my CLI tools wrapped in Docker

vim_config

My personal vim configuration

vitessce

Vitessce is a visual integration tool for exploration of spatial single-cell experiments.

webatlas-pipeline

workflow-assign-peaks-to-cells

workflow-xenium