Pinned Repositories
Qupath_to_LMD
Code to facilitate translation of QuPath annotations to LMD compatible contours
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
DVP
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.
P12E11_AshlarQC
puncta-dynamics
josenimo's Repositories
josenimo/06_QuPath_Annotation_to_AnnData
annotate cells wether they are inside a QuPath annotation. Expects QuPath geojson export from the same image.
josenimo/cylinter
An Interactive Image Segmentation Filter for Multiplex Microscopy
josenimo/DVP
josenimo/mcmicro
Multiple-choice microscopy pipeline
josenimo/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
josenimo/napari-cell-gater
A napari plugin for cell marker gating.
josenimo/nf-core-mcmicro
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
josenimo/P12E11_AshlarQC
josenimo/puncta-dynamics
josenimo/PyProteomics
Python functions to analyze proteomic data
josenimo/Qupath_to_LMD
josenimo/Qupath_to_LMD_v2
Code to facilitate translation of QuPath annotations to LMD compatible contours
josenimo/Rosalind
josenimo/scimap
This is a repo that will implement scimap from labsyspharm/scimap and add CLI for different tools
josenimo/SOPA_Cellpose
josenimo/test-datasets-modules
Test data to be used for automated testing with the nf-core pipelines