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