Jose Nimo's repositories
napari-cell-gater
A napari plugin for cell marker gating.
Language:PythonBSD-3-Clause000
mcmicro
Multiple-choice microscopy pipeline
Language:NextflowMIT000
PyProteomics
Python functions to analyze proteomic data
Language:Jupyter NotebookGPL-3.0000
Qupath_to_LMD_v2
Code to facilitate translation of QuPath annotations to LMD compatible contours
Language:Jupyter NotebookGPL-3.0000
Language:HTMLGPL-3.0000
cylinter
An Interactive Image Segmentation Filter for Multiplex Microscopy
Language:PythonMIT000
nf-core-mcmicro
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Language:NextflowMIT000
scimap
This is a repo that will implement scimap from labsyspharm/scimap and add CLI for different tools
Language:PythonMIT000
test-datasets-modules
Test data to be used for automated testing with the nf-core pipelines
MIT000
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
Language:NextflowMIT000
Language:Jupyter Notebook000
06_QuPath_Annotation_to_AnnData
annotate cells wether they are inside a QuPath annotation. Expects QuPath geojson export from the same image.
Language:Jupyter Notebook000
Language:Jupyter Notebook000