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)
py-imcyto
IMC segmentation in python.
sparks
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/Etch-a-Cell-Nuclear-Envelope
FrancisCrickInstitute/babs_uv_polymerase
Simulator of polymerase dynamics during UV damage and repair
FrancisCrickInstitute/tumour-growth-patterns-impact-evolution
Agent-based modelling reveals the impact of growth patterns on spatial and temporal features of clonal diversification. A GitHub repository of the Source Code for the model and Source Data for the figures of the paper.
FrancisCrickInstitute/vanMaldegem_Valand_2021
Code associated with Van Maldegem & Valand et al. 2021, for the analysis of Imaging Mass Cytometry data
FrancisCrickInstitute/4-Stepper-motor-control-board
Board to control 4 stepper motors based on the Teesny 3.5 dev. board. It has a small OLED display and 4 rotary encoders with switch and 2 DAC outputs in BNC connectors.
FrancisCrickInstitute/babs_recruit_2021
Recruitment questions for 2021 vacancy
FrancisCrickInstitute/Lattke_et_al_Astrocyte_Maturation
FrancisCrickInstitute/mitoem-challenge
FrancisCrickInstitute/network-syslog-summary
Summarise syslog-ng format Cisco logs and graph count. Post results to Slack.
FrancisCrickInstitute/pcr-lambda-test
FrancisCrickInstitute/StepperController
Controller board for stepper motors
FrancisCrickInstitute/Chromosome-Condensation
A simple biophysical model for chromosome condensation simulations
FrancisCrickInstitute/Chromosome_modelling
C++ software tool for 3D chromosome modelling using HiC data
FrancisCrickInstitute/its-github-guidance
A place for best practice, hints and tips
FrancisCrickInstitute/anabfem
Finite element analysis of annular ablation experiments
FrancisCrickInstitute/biologicSC
FrancisCrickInstitute/biologicViewerSC
A single-cell Visualization tool for Seurat objects
FrancisCrickInstitute/CellProfiler
An open-source application for biological image analysis
FrancisCrickInstitute/hatchet
HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
FrancisCrickInstitute/imcyto
Image Mass Cytometry analysis pipeline
FrancisCrickInstitute/Kilosort2
Fast spike sorting with drift correction for up to a thousand channels
FrancisCrickInstitute/Legacy_Power
FrancisCrickInstitute/luslab.github.io
Main documentation and "play-book" for the London Luslab
FrancisCrickInstitute/network_modules
Modules used by the IT&S Networks team
FrancisCrickInstitute/Pachnis-lab
FrancisCrickInstitute/PBMC10k
FrancisCrickInstitute/reframe
A regression testing framework to facilitate the sanity checking of HPC systems.
FrancisCrickInstitute/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
FrancisCrickInstitute/scrnaseq-datachallenge
The Crick's Bioinformatics and Biostatistics group scRNA-seq interview data challenge
FrancisCrickInstitute/spyking-circus-camp