The Francis Crick Institute

OmeSliCC

Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)

TRACERx-PHLEX

Modular pipeline for integrated analysis of the tumour microenvironment using multiplex imaging

Making-Lab-Repositories

Segment-Flow

Nextflow pipeline for deep learning segmentation models

spherical-phenotype-clustering

Cole_2024

Code associated with Cole et al. 2024

deep-imcyto

Nextflow pipeline for IMC segmentation tasks.

TRACERxIMCSpillover

Spillover plugins for TRACERx imaging mass cytometry data analysis, adapted from Chevrier et al 2018.

chronogram

cast and annotate metadata, laboratory & clinical data

network_invsync

Verify ISE and YAML inventory are synchronized

TWOMBLI

A ImageJ Plugin implementation of TWOMBLI

UK_TRE

For documents and activity records completed within Working Groups lead by Pete Barnsley (Francis Crick Institute) within the UK TRE community

AIoD-Model-Registry

The core registry for all AI models available on AI on Demand

AnaFind

Analyse-Midbodies

Bar_seq

Bpod_Gen2

Repository for 2nd generation Bpod platform (formerly beta branch of Bpod repository)

CALM

Crick Advanced Light Microscopy

CALM_Template

hts_neutralisation_launcher

Automate neutralisation analyses

mito-synapto-spine-analysis

MT_Force_Spindle

Public codes for Chu et al.,

Multichannel_photodiode

PARSEG

A novel approach to tackle overlapping segmentation in bioimages. Vanessa Dao, ELMI 2024

PooledPEScreen

Accompanying code to "High-throughput screening of human genetic variants by pooled prime editing"

segment-anything

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

sparks-ai

uniprot_annotation

A script to collect residue annotations for a list of proteins using the UniProt ID mapping tool

VHL-SGE

Code for processing of SGE data sets and all analyses included in "Saturation Genome Editing Resolves the Functional Spectrum of Pathogenic VHL Alleles"

Yeast-Oris

Genomic origins-of-replication and ROC motif co-cooccurrence analysis in yeast