Pinned Repositories
ActiveUnetSegmentation
Unet implementation to work with active contours for segmentations. Using keras and tensorflow 1.15 or 2.5.
cbias-napari
Introduction to Napari training course
Etch-a-Cell-Nuclear-Envelope
napari-tutorial
Modular course teaching the use of napari for image visualisation and analysis
network_borg_blog
Network Borg Blog - Resistance is futile *** Blog Edition - Not Maintained! ***
OmeSliCC
Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
PEACE_melanoma_14_paper
py-imcyto
IMC segmentation in python.
TRACERx-PHLEX
Modular pipeline for integrated analysis of the tumour microenvironment using multiplex imaging
warpAnnotations
A tool to transform annotations (such as points, skeletons or meshes) between spatial datasets.
The Francis Crick Institute's Repositories
FrancisCrickInstitute/TRACERx-PHLEX
Modular pipeline for integrated analysis of the tumour microenvironment using multiplex imaging
FrancisCrickInstitute/OmeSliCC
Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
FrancisCrickInstitute/sparks
FrancisCrickInstitute/image-analysis-outreach
A collection of materials and information for school outreach sessions about image analysis
FrancisCrickInstitute/Making-Lab-Repositories
FrancisCrickInstitute/Segment-Flow
Nextflow pipeline for deep learning segmentation models
FrancisCrickInstitute/spherical-phenotype-clustering
FrancisCrickInstitute/CALM
Crick Advanced Light Microscopy
FrancisCrickInstitute/Cole_2024
Code associated with Cole et al. 2024
FrancisCrickInstitute/multi-dimensional-imaging-and-analysis
FrancisCrickInstitute/chronogram
cast and annotate metadata, laboratory & clinical data
FrancisCrickInstitute/TWOMBLI
A ImageJ Plugin implementation of TWOMBLI
FrancisCrickInstitute/3D-printer-simulator
3D printer simulator
FrancisCrickInstitute/AIoD-Model-Registry
The core registry for all AI models available on AI on Demand
FrancisCrickInstitute/AnaFind
FrancisCrickInstitute/Analyse-Midbodies
FrancisCrickInstitute/Bpod_Gen2
Repository for 2nd generation Bpod platform (formerly beta branch of Bpod repository)
FrancisCrickInstitute/CALM_Template
FrancisCrickInstitute/hts_neutralisation_launcher
Automate neutralisation analyses
FrancisCrickInstitute/image-analysis-grid
Outreach project on image analysis, run by EM STP, with SE&AI and CALM STPs
FrancisCrickInstitute/Multichannel_photodiode
FrancisCrickInstitute/nextflow-modules
Contains managed modules and subworkflows for Nextflow that can be installed into pipelines
FrancisCrickInstitute/PARSEG
A novel approach to tackle overlapping segmentation in bioimages. Vanessa Dao, ELMI 2024
FrancisCrickInstitute/PooledPEScreen
Accompanying code to "High-throughput screening of human genetic variants by pooled prime editing"
FrancisCrickInstitute/python-decon
FrancisCrickInstitute/rgb-colour-slider
Colour slider activity to teach how RGB colours combine
FrancisCrickInstitute/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.
FrancisCrickInstitute/sparks-ai
FrancisCrickInstitute/uniprot_annotation
A script to collect residue annotations for a list of proteins using the UniProt ID mapping tool
FrancisCrickInstitute/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"