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background_subtraction

Background subtraction for COMET platform

histocat

Histology Topography Cytometry Analysis Toolbox

imc2mc

staging of imc images for mcmicro

infrastructure

All of Galaxyproject EU's cloud infrastructure.

infrastructure-playbook

Ansible playbook for managing UseGalaxy.eu infrastructure. For the playbook managing Galaxy itself, see https://github.com/galaxyproject/usegalaxy-playbook/

kbestak_lab-rotation

Lab rotation report 2/2022 – 4/2022, Krešimir Beštak

mask2bbox

Useful tools for converting segmentation masks into bounding box objects.

mcmicro

Multiple-choice microscopy pipeline

mcmicro-celesta

CELESTA phenotyping module for MCMICRO

mcmicro_hackathon_2022

Website for the MCMICRO hackathon 2022

mcmicro_nfcore_demo

A small demo workflow for MCMICRO using only nf-core modules. Result of the March 2023 nf-core hackathon.

mcmicro_qc

Module to prepare QC output from MCMICRO for MultiQC.

mcmicrogui

Interactive report for MCMICRO

melanoma_brain_metastasis

mi_spatialomics

Data analysis for “Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration”

micronuclai

Automated identification of micronuclei for chromosomal instability (CIN) quantification.

micronuclai_labeling

micronuclai_streamlit

This repository contains a streamlit app for CIN inferences based on the micronuclAI tool

mindagap

Fill empty grids of a panorama made from several tiles with sensefull values (mean of imediate neighbourhood)

molkart-local

Repository for local modules used in nf-core/molkart

multiplex_macsima

utitilies for macsima image sets

norm_methods

A single repo of all available/potential tabular normalization methods for downstream analysis of spatial proteomics datasets.

palom

Piecewise alignment for layers of mosaics

phenoimager2mc

Formatting tif/ome-tif metadata for MCMICRO staging modules

quantification

Quantification module for mcmicro

scimap

This is a repo that will implement scimap from labsyspharm/scimap and add CLI for different tools

segmentation_prep

Image preprocessing for different segmentation approaches.

smfish_analysis_mi

Analysis of RNAscope images for human MI samples for Kuppe, Ramirez et al 2022.

spatialomicsoverview

spot2cell

Tool to assign FISH spots to their corresponding cell